I don't know how, but it is working now. Since I am just getting started with Perl I am satisfied unless it breaks again. The next paragraph is probably useless to you. Thanks perldiag and andrew.

I played around with splain and I saw some strange stuff where the first characters of the second line were being replaced with the heredoc delimiter string. I was about to post some copies of those results on here, so I changed the code back to what I posted earlier for the sake of consistency. Now it is magically working. Padre did crash when I was doing this, so I think that Padre somehow corrupted the file (??) and the corruption was invisible to me but it was manifesting in the results from padre's run button and the command line execution.