Slow synchronisation between Desktop-Client and Server?

The difference for a lot of small files is that your database needs to create a lot of entries. You can optimize your mysql settings with help of scripts like tuning-primer.sh. I did some test in the past where I found some parameters that can increase the speed considerably, part is the innodb_flush-stuff that @victorbw mentioned (however there is a risk that some queries will be lost in case your server crashes):

I should run this tests again with the current version of NC.