Signal tap II issue

SignalTap is based on digital logic, so it either captures a 1 or a 0. (It could go metastable, but that won't show up in the SignalTap waveform. And since captured data just feeds a large capture buffer, it's unlikely to cause any problems at all, since the fanout is probably 1 the whole way...)

The numbering on the top is your clock edge. Your sampling with a clock that is much faster than most of the signals, but when they transition a lot, it looks like that. Zoom in and you should see clean values for each clock. (Looks like you have a pretty deep buffer size...)