So I put this original post up ages ago.
Client is still buggy (Has had this bug along with numerous other bugs for ages now) that are just ignored with all the focus on just constantly adding new functionality, which I understand they need to focus on, but it is a shame as well, because core things just aren’t implemented well that need fixing.
For anyone that is frustrated by this bug, you can disable bulk uploads (packing 100 files at a time) by adding this in your server config file:
'bulkupload.enabled' => false
By adding that line, it disables packing up 100 files into a single upload… Obviously, packing small files into a single upload SHOULD make it faster, as it eliminates the latency between each file, but something is broken somewhere and for me, a transfer that would have taken about 5 days came down to a few hours (over 100,000 small files)
You may have to restart the client afterwards, not sure… I restarted mine to make sure it picked up the change, but it may just detect it on next sync without a restart, not sure?