This is just a guess at this point (just got off work and I'm still sober), and I probably ought to double check the man page, but I'm pretty sure that chomp() will remove only a single whitespace character from the end of the line. Even though the \r\n pair might be considered a single char in other contexts, it is two distinct characters so far as chomp() is concerned.
Update: Well, I guess I just stuck my foot in my mouth. I just checked the man page and it says:
This safer version of chop removes any trailing string that corresponds to the current value of $/ (also known as $INPUT_RECORD_SEPARATOR in the English module).
So kindly disregard my guess. :)
On time, cheap, compliant with final specs. Pick two.