It's probably only CR LF. The LF was converted to CR LF by Perl since you didn't binmode(STDOUT).

You could do:

while (<$fh>) {
   s/\x0D\x0A\z//;
   ...
}
[download]

Or change $/:

local $/ = "\x0D\x0A";
while (<$fh>) {
   chomp;
   ...
}
[download]

Or if you don't care about whitespace at the end of the line, the following works with CR CR LF and CR LF:

while (<$fh>) {
   s/\s+$//;
   ...
}
[download]