Without more information -- such as error messages, warnings and any logged info -- it's hard to guess what's wrong. BUT since, if I understand you correctly -- your script didn't work on Windows when invoked from the command line, of course it's not going to work when converted to an exe with 'paker (sic)', Coro or any other mechanism.

Nonetheless, and to give you an easy way to start seeking out the problem, you might want to check (CPAN, CPANTesters, bioperl, inter alia) whether all the modules you're using are compatible with Windows. (If any have xs components, the liklihood that they'll work on W32 starts to approach 0%.)

But when you've done your due diligence, come back and show us the script, the errors, warnings, log entries and exactly how (and where) you packed the sources into an exe.

P.S. spelling counts. The misspellings in your node will make it hard to find using normal search techniques for future visitors with similar problems.