Your .pl file association is correct in regards to executing the script, but is incorrect/incomplete because it doesn't "see" the args passed to the script.
Look up the HKEY_CLASSES_ROOT\Applications\perl.exe\shell\open\command entry in the registry. The value should be "C:\Perl\bin\perl.exe" "%1". I suspect that yours is missing the "%1"
EDIT: Sorry, I just saw your .pl association post. It looks correct.
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