Signal Tap Problem: Some signals have jitter

Nyquist-Shannon theorem should be applied when converting analog signal to digital. In your case you already are working with digital signals. So as josyb said no need to involve any theorems here. Jitter that you are seeing is from timing violations (Setup and Hold) which are caused because you are sampling your signals with clock which is asynchronous to them. For signaltap as a sampling clock you have to chose synchronous clock to your signals and thats it.