Linux – Command line PHP script no longer working

A previously working command line PHP script has stopped working – when i run it now it returns this error:

[root@server dir]# ./custom.php
Extension './custom.php' not present.

If i run the script like this it works:

[root@server dir]# php custom.php

For a number of reasons i cannot do this though. I have read something that implies this could be related to line endings but no idea how/why. i have edited this file recently on A Mac and a PC and FTP'd it to the server but i've been doing that for a long time without issues.

EDIT First line of script is:

#!/usr/bin/php -q

FYI The server is running CentOS 5.4