The most confusing (non-perl) bug I've have to deal with was when someone tried using Dreamweaver to ftp a file to a remote webserver, and the file contents were stomped on (zero file size).
I then realised that the local file had also been stomped on.
I eventually realised that they'd mapped a drive (windows) to the remote webserver, and were editing the remote file directly in Dreamweaver...
...which had tried to upload over itself...