That's not quite enough information. I use Winamp to make MP3s as well. However, I use a plugin called "out_mp3" that relies on a codec being installed on the system for it to work. Are you using the embedded encoder that's part of Winamp? Are you using Winamp Pro? What speed is your CPU (this shouldn't make a difference. I've encoded USFs to MP3s on a 333, where the song I was encoding simply required more CPU than I had. Even though in normal play it was terribly choppy, it sounded just fine in MP3)? What USF set are you trying to encode? I'd say it's possible that the kHZ is messing up Winamp's encoder. For example, Mario Kart has a really weird refresh rate.
In the end, my suggestion is to try out different encoding software. I know there's tons out there. I have 2 or 3 different ways to make MP3s on my PC, all of which were free. I'm sure you can find something as well. Hopefully though, HCS will be able to give you a clearer answer. Mouser X over and out.