It sounds like the carriage return is still in the file on the linux side. If you ftp'ed the file from windows to linux in binary mode, that would be the case. Do a little test case such as this:

#!/usr/bin/perl -wd

while(<>) {
        chomp;
        print $_, "\n";
}
[download]

While in the debugger, display $_ (x $_) after the chomp. Do you see something like this: "blah blah blah\cM"? That control-M is the carriage return. Some editors may also show the carriage return (vi) if configured properly. chomp removes any trailing string that corresponds to the current value of $/. In this case only the unix newline will be removed. You could be more destructive and remove all whitespace at the end of a line with a regex such as s/\s+$//. That would work on both platforms and you wouldn't have to worry. Or you could ensure your transfer process does the correct translation for you.

-derby