I upgraded to version 4.3.5 and then a week later to 4.3.6 hoping it would correct the kinds of problems you describe.
It did not. I was unable to synchronize file system, there were permissions issues for files. Now even administrators on their own sites get the message "You don't have permission to see the files on the site."
I truncated the Files and Folders table and re-synched files, having to go to each portal to do so. I am not convinced that the files all got re-synched. What is worse, in many (though not most) instances, image modules display wrong images - from entirely different folders though fortunately from the same portal.
I had file system synchronization scheduled and it shows failure after failure.
I figured then I would export the sites and set them up on a new install. But I cannot do a portal export to a template due to file system problems.
This is quite a mess.
Does anyone know how to remedy this? Rebuilding the sites from scratch would be extremely painful. Even using templates it would not be a lot of fun for two sites in particular.
Some guidance would be most welcome.