zero: I should mention it because it's not obvious, but the problem with the symlinks turned out to be a creation problem. When the \r wasn't being removed from the end of the ! line in the EXEC module the !vfs:chattr function got a double quoted string with the \r on the end so it failed to remove both the \r and the double quotes so the link was wrong. I should have noticed the target from the site chattr +l command having quotes around it, but just thought that was the way it should be displayed... It's fixed now but the existing links will still be wrong (though with it deleting all files on upload it's unlikely you had a lot of them).
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