I have one portal that has encountered this issue twice. I wanted to find out if anyone had any insight into the cause/resolution of the problem.
For one portal only, the Portal Root folder and all subfolders are losing all of their permissions (the only permissions left are the Administrator permissions). In addition, this is causing anything that a file was selected from the drop-down list (Downloads module, site logo, etc) to "break".
The one thing that I noticed about this portal is that there was a /Portals/23 set of folders within that portal's root (and this portal is portal 23).
I have deleted the extra folder and also disabled the Synchronization task.