I think i got a similar error after upgrading from 9.0.51 to 9.0.52
{"reqId":"Uv1AyJjmEmx1S8PFE\/Pr","remoteAddr":"185.22.x.x","app":"index","message":"Exception: {\"Exception\":\"OCP\\\\AutoloadNotAllowedException\",\"Message\":\"Autoload path not allowed: \\\/var\\\/www\\\/nextcloud\\\/apps\\\/theming\\\/lib\\\/template.php\",\"Code\":0,\"Trace\":\"#0 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/autoloader.php(172): OC\\\\Autoloader->isValidPath('\\\/var\\\/www\\\/nextcl...')\\n#1 [internal function]: OC\\\\Autoloader->load('OCA\\\\\\\\Theming\\\\\\\\Tem...')\\n#2 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/server.php(569): spl_autoload_call('OCA\\\\\\\\Theming\\\\\\\\Tem...')\\n#3 \\\/var\\\/www\\\/nextcloud\\\/3rdparty\\\/pimple\\\/pimple\\\/src\\\/Pimple\\\/Container.php(113): OC\\\\Server->OC\\\\{closure}(Object(OC\\\\Server))\\n#4 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/appframework\\\/utility\\\/simplecontainer.php(102): Pimple\\\\Container->offsetGet('ThemingDefaults')\\n#5 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/servercontainer.php(87): OC\\\\AppFramework\\\\Utility\\\\SimpleContainer->query('ThemingDefaults')\\n#6 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/server.php(1227): OC\\\\ServerContainer->query('ThemingDefaults')\\n#7 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/template.php(79): OC\\\\Server->getThemingDefaults()\\n#8 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/base.php(308): OC_Template->__construct('', 'update.user', 'guest')\\n#9 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/base.php(924): OC::checkMaintenanceMode()\\n#10 \\\/var\\\/www\\\/nextcloud\\\/index.php(39): OC::handleRequest()\\n#11 {main}\",\"File\":\"\\\/var\\\/www\\\/nextcloud\\\/lib\\\/autoloader.php\",\"Line\":152}","level":3,"time":"2016-07-06T10:09:33+00:00","method":"GET","url":"\/","user":"--"}
{"reqId":"Uv1AyJjmEmx1S8PFE\/Pr","remoteAddr":"185.22.x.x","app":"core","message":"Exception: {\"Exception\":\"OCP\\\\AutoloadNotAllowedException\",\"Message\":\"Autoload path not allowed: \\\/var\\\/www\\\/nextcloud\\\/apps\\\/theming\\\/lib\\\/template.php\",\"Code\":0,\"Trace\":\"#0 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/autoloader.php(172): OC\\\\Autoloader->isValidPath('\\\/var\\\/www\\\/nextcl...')\\n#1 [internal function]: OC\\\\Autoloader->load('OCA\\\\\\\\Theming\\\\\\\\Tem...')\\n#2 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/server.php(569): spl_autoload_call('OCA\\\\\\\\Theming\\\\\\\\Tem...')\\n#3 \\\/var\\\/www\\\/nextcloud\\\/3rdparty\\\/pimple\\\/pimple\\\/src\\\/Pimple\\\/Container.php(113): OC\\\\Server->OC\\\\{closure}(Object(OC\\\\Server))\\n#4 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/appframework\\\/utility\\\/simplecontainer.php(102): Pimple\\\\Container->offsetGet('ThemingDefaults')\\n#5 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/servercontainer.php(87): OC\\\\AppFramework\\\\Utility\\\\SimpleContainer->query('ThemingDefaults')\\n#6 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/server.php(1227): OC\\\\ServerContainer->query('ThemingDefaults')\\n#7 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/template.php(79): OC\\\\Server->getThemingDefaults()\\n#8 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/base.php(308): OC_Template->__construct('', 'update.user', 'guest')\\n#9 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/base.php(924): OC::checkMaintenanceMode()\\n#10 \\\/var\\\/www\\\/nextcloud\\\/index.php(39): OC::handleRequest()\\n#11 {main}\",\"File\":\"\\\/var\\\/www\\\/nextcloud\\\/lib\\\/autoloader.php\",\"Line\":152}","level":3,"time":"2016-07-06T10:09:33+00:00","method":"GET","url":"\/","user":"--"}
{"reqId":"Uv1AyJjmEmx1S8PFE\/Pr","remoteAddr":"185.22.x.x","app":"core","message":"Exception: {\"Exception\":\"OCP\\\\AutoloadNotAllowedException\",\"Message\":\"Autoload path not allowed: \\\/var\\\/www\\\/nextcloud\\\/apps\\\/theming\\\/lib\\\/template.php\",\"Code\":0,\"Trace\":\"#0 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/autoloader.php(172): OC\\\\Autoloader->isValidPath('\\\/var\\\/www\\\/nextcl...')\\n#1 [internal function]: OC\\\\Autoloader->load('OCA\\\\\\\\Theming\\\\\\\\Tem...')\\n#2 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/server.php(569): spl_autoload_call('OCA\\\\\\\\Theming\\\\\\\\Tem...')\\n#3 \\\/var\\\/www\\\/nextcloud\\\/3rdparty\\\/pimple\\\/pimple\\\/src\\\/Pimple\\\/Container.php(113): OC\\\\Server->OC\\\\{closure}(Object(OC\\\\Server))\\n#4 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/appframework\\\/utility\\\/simplecontainer.php(102): Pimple\\\\Container->offsetGet('ThemingDefaults')\\n#5 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/servercontainer.php(87): OC\\\\AppFramework\\\\Utility\\\\SimpleContainer->query('ThemingDefaults')\\n#6 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/server.php(1227): OC\\\\ServerContainer->query('ThemingDefaults')\\n#7 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/template.php(79): OC\\\\Server->getThemingDefaults()\\n#8 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/template.php(339): OC_Template->__construct('', 'exception', 'error', false)\\n#9 \\\/var\\\/www\\\/nextcloud\\\/index.php(55): OC_Template::printExceptionErrorPage(Object(OCP\\\\AutoloadNotAllowedException))\\n#10 {main}\",\"File\":\"\\\/var\\\/www\\\/nextcloud\\\/lib\\\/autoloader.php\",\"Line\":152}","level":3,"time":"2016-07-06T10:09:33+00:00","method":"GET","url":"\/","user":"--"}
oc_appconfig does look like:
MariaDB [nextcloud]> select * from oc_appconfig
-> ;
+----------------------+----------------------------------+---------------------------------+
| appid | configkey | configvalue |
+----------------------+----------------------------------+---------------------------------+
| activity | enabled | yes |
| activity | installed_version | 2.2.1 |
| activity | types | filesystem |
| admin_audit | enabled | yes |
| admin_audit | installed_version | 1.0.0 |
| admin_audit | types | logging |
| announcementcenter | enabled | no |
| announcementcenter | installed_version | 1.1.2 |
| announcementcenter | ocsid | 173921 |
| announcementcenter | signed | true |
| announcementcenter | types | |
| backgroundjob | lastjob | 1 |
| bookmarks | enabled | no |
| bookmarks | installed_version | 0.7 |
| bookmarks | ocsid | 168710 |
| bookmarks | types | |
| calendar | enabled | no |
| calendar | installed_version | 1.2.2 |
| calendar | ocsid | 168707 |
| calendar | types | |
| comments | enabled | yes |
| comments | installed_version | 0.2 |
| comments | types | logging |
| contacts | enabled | no |
| contacts | installed_version | 1.3.1.0 |
| contacts | ocsid | 168708 |
| contacts | types | |
| core | backgroundjobs_mode | cron |
| core | installedat | 1467305308.0274 |
| core | lastcron | 1467798305 |
| core | lastupdateResult | [] |
| core | lastupdatedat | 0 |
| core | oc.integritycheck.checker | [] |
| core | public_files | files_sharing/public.php |
| core | public_webdav | dav/appinfo/v1/publicwebdav.php |
| core | remote_caldav | dav/appinfo/v1/caldav.php |
| core | remote_calendar | dav/appinfo/v1/caldav.php |
| core | remote_carddav | dav/appinfo/v1/carddav.php |
| core | remote_contacts | dav/appinfo/v1/carddav.php |
| core | remote_dav | dav/appinfo/v2/remote.php |
| core | remote_files | dav/appinfo/v1/webdav.php |
| core | remote_webdav | dav/appinfo/v1/webdav.php |
| core | repairlegacystoragesdone | yes |
| core | shareapi_allow_mail_notification | yes |
| core | shareapi_default_expire_date | yes |
| core | shareapi_exclude_groups | no |
| core | shareapi_exclude_groups_list | [""] |
| core | umgmt_show_email | true |
| core | umgmt_show_last_login | true |
| dav | enabled | yes |
| dav | installed_version | 0.1.6 |
| dav | types | filesystem |
| external | enabled | yes |
| external | installed_version | 1.2 |
| external | ocsid | 166046 |
| external | types | |
| federatedfilesharing | enabled | yes |
| federatedfilesharing | installed_version | 0.1.0 |
| federatedfilesharing | types | |
| federation | enabled | yes |
| federation | installed_version | 0.0.4 |
| federation | types | authentication |
| files | cronjob_scan_files | 500 |
| files | default_quota | 5 GB |
| files | enabled | yes |
| files | installed_version | 1.4.4 |
| files | types | filesystem |
| files_pdfviewer | enabled | yes |
| files_pdfviewer | installed_version | 0.8.1 |
| files_pdfviewer | ocsid | 166049 |
| files_pdfviewer | types | |
| files_sharing | enabled | yes |
| files_sharing | installed_version | 0.9.1 |
| files_sharing | types | filesystem |
| files_texteditor | enabled | yes |
| files_texteditor | installed_version | 2.1 |
| files_texteditor | ocsid | 166051 |
| files_texteditor | types | |
| files_trashbin | enabled | yes |
| files_trashbin | installed_version | 0.8.0 |
| files_trashbin | types | filesystem |
| files_versions | enabled | yes |
| files_versions | installed_version | 1.2.0 |
| files_versions | types | filesystem |
| files_videoplayer | enabled | yes |
| files_videoplayer | installed_version | 0.9.8 |
| files_videoplayer | types | |
| firstrunwizard | enabled | yes |
| firstrunwizard | installed_version | 1.1 |
| firstrunwizard | ocsid | 166055 |
| firstrunwizard | types | |
| gallery | enabled | yes |
| gallery | installed_version | 14.5.0 |
| gallery | types | |
| music | enabled | no |
| music | installed_version | 0.3.11 |
| music | ocsid | 164319 |
| music | types | filesystem |
| news | enabled | no |
| news | installed_version | 8.8.0 |
| news | ocsid | 168040 |
| news | types | |
| notes | enabled | no |
| notes | installed_version | 2.0.1 |
| notes | ocsid | 174554 |
| notes | types | |
| notifications | enabled | yes |
| notifications | installed_version | 0.2.3 |
| notifications | types | logging |
| ownbackup | enabled | no |
| ownbackup | installed_version | 0.3.8 |
| ownbackup | ocsid | 170674 |
| ownbackup | types | |
| password_policy | enabled | yes |
| password_policy | installed_version | 1.0.0 |
| password_policy | types | |
| provisioning_api | enabled | yes |
| provisioning_api | installed_version | 0.4.1 |
| provisioning_api | types | prevent_group_restriction |
| shorten | enabled | no |
| shorten | installed_version | 0.0.15 |
| shorten | ocsid | 168591 |
| shorten | types | filesystem |
| systemtags | enabled | yes |
| systemtags | installed_version | 0.2 |
| systemtags | types | logging |
| tasks | enabled | no |
| tasks | installed_version | 0.9.1 |
| tasks | ocsid | 164356 |
| tasks | types | |
| templateeditor | enabled | yes |
| templateeditor | installed_version | 0.1 |
| templateeditor | types | |
| theming | enabled | yes |
| theming | installed_version | 0.1.0 |
| theming | types | |
| updatenotification | enabled | yes |
| updatenotification | installed_version | 0.1.0 |
| updatenotification | types | |
+----------------------+----------------------------------+---------------------------------+
139 rows in set (0.00 sec)