It might be a owner Group permission issue.
Just guessing.
When you ftp to your files you will see besides the file/folder permissions, A number for a owner/group.
That number should be the same for every file and folder you have.
If some are different you will need to contact your host.
I can't remember the exact symptoms I had but what happened was the host upgraded the server and some files were changed to a group I could not access so some scripts would not execute.
Other than that maybe you have a couple of corrupted files?????
