Yep ... in the Windows world, things can be a bit messy. Many Windows users simply replace chomp $varname; with $varname =~ s/\s+$//; to trim off all trailing whitespace from a variable.

NOTE: It's not an exact replacement, so if your code expects whitespace at the end of your lines, you'll probably want to adjust $/ to the proper value for your incoming files. For my purposes, removing whitespace from the end of the string works fine in nearly all cases.