SignalTap sampling issues

When nothing makes sense, check your basics first. Depending on how new the board design is, check: Power supply voltages, reference clock(s) to the part, and the locked signal of the PLL clock you are using for the capture. Check timing closure, and try to focus on sampling registered signals if you can. If you have pulled a bunch of test signals to pins, like it sounds you may have, bring out the capture clock and check it thoroughly on a scope. If the foundations are solid, then it will be a little more tricky / intriguing to straighten out. I love/hate signal tap and use it often as well. Still I always bring out a full MICTOR connector worth of test pins.