Are you sure there aren't any other locations that your server is using to publish files from? Any temp directories or anything like that that you may not know of. Heres what i would do:
1. Get a nice session going on your Front end connection and try to get a couple of the errors.
2. Try to find all the most recently modified files and see what the permissions are on those directories and parent directories.
3. See if you can 755 those out and try to troubleshoot from there.
Good luck, nothing fun about sporadic hard to replicate errors, but all the easy ones have already been solved