I will try to configure SignalTap with multiple domains and see. The odd thing is that I have never seen this before - even with multiple clock domains.
SignalTap was working perfectly on this project until I added a DDR controller and since then, for some compiles signaltap works, for others it does not. I have had other designs in the past with DDR and had no issues with signal tap. First I thought it was my cable, but that was not the issue because I tried it on a different project - same board though.
Yes, I did specify the fastest clock in my design just to avoid trigger misses. The missed trigger happens whether I put it on a signal from a slow domain or the same domain as the sampling clock.