How about posting a small code snippet that shows the problem. I suggest you use the following template as a starting point:

use strict;
use warnings;

while (<DATA>) {
    chomp;
    print ">$_<\n";
}

__DATA__
test data that chomps fine.
Your manky data that fails for a chomp
A nicely chomped line
[download]

Prints:

>test data that chomps fine.<
>Your manky data that fails for a chomp<
>A nicely chomped line<
[download]