2 other options to check, i know a friend of mine swore that the permission where set on his FTP client, but when i looked via cpanel they were not, so his ftp was showing something different than what was actually the case.

#2 have you set the chmod via SSH shell access? i did this with 4 sites and one of them threw back an error and set the whole domain to permissions to 0
so i couldnt set them via cpanel either as i was no longer the owner of the account.

this is a dedicated server i am see more using.