Glad I came across this post as it gave me a clue as to what the issue could be. I have a bit a different case but it's related to recording as well and I was able to fix it.
I was using Soundtrack Pro (vers. 2.0.2/ Final Cut Studio 2) for the first time to record and experienced a distortion/delay issue as well. I'm recording from a turntable (Stanton T.92USB) with USB output, to digitize my vinyl collection. Out of the box, I plugged it in, fired up STP, hit record and everything worked like a charm. I noticed though, that it recorded at 44.1kHz even though the project was set to 48kHz. So I tried to find out why as the turntable should be able to output 48kHz. I clicked on the "Device Setup" in STP which launches the "Audio MIDI Setup" application from the Utilities folder. Indeed, the default input from the turntable was set to 44.1kHz, so I switched it to 48kHz. That's probably when things got hairy.
Going back to STP, trying to record again, the signal I got in sounded like there was tons of dust on the record and the needle would jump intermittently. The record I had just cleaned and by looking at the needle, it didn't seem to jumping either... and I just recorded the song couple minutes ago and everything was fine. So I didn't quite understand what the issue was. I deleted the STP prefs and checked under "Device Setup" that everything was back to 44.1kHz but I still had the distortion. So I thought it would be related to the turntable or the needle. I tried other records and all sounded distorted and jumpy.
Seeing this post where you said that QuickTime recorded fine, I tried that as well and that did work just fine. So I knew the Audio Units must have gotten messed up when changing the input. For some reason, this only seemed to have affected STP and not systemwide. Anyways, in order to reset weird cache issues, is to use OnyX, a free Mac system utility. Here is what I did: open OnyX, go to "Cleaning" tab, under "System" only select Audio Components, under "User" only select Audio Units, under the remaining tabs "Internet, Fonts, Logs, Misc" disable everything and then hit "Execute". This will require a restart. After that, everything was back to normal for me.
So my guess is, if you do have external Audio hardware that you need to configure in the "Audi MIDI Setup", there might be a bug in Snow Leopard that affects Soundtrack Pro. Maybe resetting the Audio Units fixes this but in any case, submit feedback for STP at
http://www.apple.com/feedback/soundtrackpro.html so it might get resolved in a future update.
Good luck~