Show us some code!

Also, if your record separator is set to "EOF", could you tell us what the value of EOF is for your OS? My experience is that explicit EOF markers aren't used in most media (iirc, they're still used for tapes, cards, and JCL) in most current O/S (even Windows pretty much ignores its ^Z EOF marker of the distant past).

So, I see a few possibilities. One is that your file has no record separators (unlikely, but possible). A second is that your version of Perl was built improperly, so it's not recognizing your O/S's record separators. Since you've said you're on a *ix, it's possible that you're processing files from a Mac, which once used \r as a record separator. The final possibility is that there is a bug in your code. The first place I look is in what I've done, so I would suggest you look to your code first, then the other possibilities.