Gamespy handles a bunch of different networking trackers. They also happen to provide their own libraries for handling that sort of thing- and recommend that you use their stuff. Now, having said this, I've talked with that bunch before and they're really not interested (or rather...weren't at the time in 2004 when I talked with them...) in working with Linux publishers. "No market, nor will there likely ever be one," was the the line I was given by one of the higher-ups at GDC 2004 when I talked with them.
With attitudes like that, I wouldn't put it past 'em to be problematic with the licensing of something going to the Linux side of things.
But, then again, I could be wrong. It's just that the odds of it being something networking related is higher as it's a problem in the server AND the client code.