It means something very, very bad has happened on the 2nd read (chunk 2) of a file descriptor.

You have several courses of action available. The best, depending on how novice you are, is to make a copy of the script, and start stripping out anything that doesn't demonstrate the problem. When you have a suitably small example, post it here. Also note what version of Perl you're using (available via perl -v), and on what platform.

One thing that's working in your favor is that this isn't a common error, which means it will likely warrant a bit more attention than usual here.