Update
If you guys can gain access to the filesystem of your server via SSH then you may be able to fix the problem yourselves.
One of the folders that wasn't appearing in my FTP client was akismet. I've just logged in via SSH, SU'd to root and then changed to the plugins directory and run...
I have the same problem, although the user/group names are different.
My server is CentOS 6.5 (fully patched to the best of my knowledge) and Plesk is 11.5.30 Update #42, last updated at April 17, 2014 03:49 AM.
In my case however it is not all folders only a select few. They were all created...