Well well well. It seems running this script using the latest ActivePerl binary works just fine! There must be something broken with Cygwin's Perl... I'll take this up with the Cygwin people. Thanks anyway.

EDIT: The problem was solved because Cygwin's perl was expecting Unix linefeeds, and my source file uses Windows CRLF. I was told that setting the environment variable

export PERLIO=crlf
[download]

solves this problem, and it did nicely. I'm also told, though, that it's a bit buggy, but in this case, it solves the mysterious difference between Cygwin Perl and ActivePerl. Cheers!