I've had a recurring issue with Soundtrack Pro that involves "skipping" during playback. Also, previewing loops doesn't work. It only happens on my G5 tower--never on my MacBook.
Turns out it's the result of ambient light getting into the optical audio ports on the back of the machine. Plugging an optical audio cable into both the in and out ports solved the problem. Don't know why it took me so long to find this article, but it worked like a charm.