in reply to Identical files, only one works?
0) Verifying that you aren't transferring the file up in Binary mode (it must be ASCII). As a side note, if you're using an older version of CuteFTP, it's been found to often transfer files in Binary, even when ASCII was selected (I can't tell you how many times this was an issue with CuteFTP when I was doing tech support for a commercial Perl product).
1) Check the file format... if it's a windows file, it could be screwing up on a Unix box due to the line feed character. Transferring in ASCII should fix that
2) Check the shebang line; the path to perl could be different than what you have
3) Check file permissions to make sure you set it as executable. Also make sure the owner and group permissions are set such that the web server has execute permissions