I'm having the same problem with SignalTap ignoring my trigger using QII 14.1. Before finding this post I got to the point of bringing my trigger signal out on a pin and triggering a logic analyzer off of it (which obviously worked just fine).
Before I go installing different versions of QII to see which one works I wanted to see if anyone had identified which versions of QII come with a working SignalTap II version.
The really odd thing is when I manually start and stop an analysis in SignalTap using version 14.1 the transitions are clearly visible in the captured data, SignalTap just does not trigger on them.