One more thing to check in your Fetch settings, regardless of OS: make sure the upload options to add file extensions are NOT checked. If you were dealing with something called something.cgi.bin, my guess is that Fetch added the '.bin' when you uploaded a script named 'something.cgi'. BTW, this also indicates you must also change to uploading as text, not binary, MacBinary, Raw Data, as the other poster mentioned.
Well since it appears we're talking of a MacPerl droplet, then it will need to be uploaded as MacBinary after all won't it? If Fetch insists on adding the .bin extension, then this can be removed after the file is uploaded simply by renaming the file on the server.
JD
