Is it even remotely possible your cgi-bin is accessed via a cgiwrapper? That could explain the 404 errors even though we can clearly see from your DirInfo they are indeed there in the cgi-bin. The only thing that contradicts that theory is the fact that cpanel is returning an error as opposed to a file not found 404 error.
Probably the only way to get this fixed is to have Infopop look at it via FTP. I'd suggest completing a support ticket via the Customer Support link to the left.