I might know what the problem is.
Shot in the dark here, but I had a weird thing happening yesterday that sounds slightly similar.
I had used audio snap to replace a snare, using SD3 as well. I noticed that below the standard keyboard notations to the left in the piano roll there were some additional labels that were not the standard thing (no letter/number, but a few things--can't remember exactly). I pressed one of the keys (using my mouse) and suddenly was hearing different notes, in sort of a rhythmic fashion, play, just going on and changing sounds. I didn't put it together at the time that it was going through all the sounds, but that's probably what I was hearing. I finally figured out how to stop it though--looked down at the bottom of the key notations and saw one which was labeled "Stop." That did the trick, and everything worked fine.
Can't say for sure your problem is in any way related, but it sure sounds similar. Let me know if you see what I describe, and if the "stop" key solves the problem?