Sounds like a line-ending problem. Try looking at the script with cat -vET.

If there's a Windows-style line end on a file, Unix will often misinterpret the "shebang" line saying where to find the interpreter as /usr/bin/perl^M, and since there isn't a program called /usr/bin/perl^M it fails. By editing that line, you may have fixed the line ending, accidentally fixing the problem.

If that's the problem, tools like dos2unix can fix it, or something like:

perl -pi.bak -e 's/\r//g' your_script
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