NEW SYSTEM:

Red Hat Linux release 9 (Shrike)
LANG=en_US.UTF-8
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Bingo. And I'll bet that if you do "perl -V" it will say "revision 5.0 version 8 subversion 0". Given this combination, the default behavior for output to a file is to assume the output data is supposed to be UTF-8 (to match the locale), with alterations applied where presumed necessary. And in the many cases where this is not the coder's real intention, the output gets messed up (sort of like the familiar "text-mode" vs. "binary-mode" output on microsoft systems). It would be instructive to see what is being added to the stream, to understand the process better.

Put the "use bytes;" pragma in the relevant block of code (or at the top of the script), until you have a chance to upgrade to a 5.8.1 or later release, where the default behavior is the more appropriate "leave data as-is during output, unless there is explicit instruction to do otherwise."