I still haven't solved this problem...
I suspect my problem has something to do with running a time-limited SOF. I'm using the Altera TSE MAC, and unfortunately, I'm at the stage where if I remove it, then I can't make any progress to test and debug my design. I've learned to keep only a handful of signals in ST - and trust it only part of the time.
Signaltapit, yes, I use the on-board blaster circuit. I tried your suggestion with the debugger tool and it never results in a failure. I set the iterations to 1000 and ran it about 10 times.
I program the chip using the standalone programmer and then run ST after that. Sometimes it works but often I get corrupted and worse, misleading waveforms. Most annoying is that it won't trigger correctly. I've never had this problem before with ST (I've done many designs - though never with a time-limited SOF). Any help appreciated.