I had a very similar problem. I had my original ECU and a separate ECU with the GMR tune. With the original ECU I never experienced detonation. With the tuned ECU, I had the same audible detonation under heavy boost (not necessarily full boost) at speed in third or fourth gear. I wouldn't get the detonation when I was driving hard through the twisties, even at WOT, but if I then drove an hour at regular freeway speeds back to the city, it would detonate. I came to two possible conclusions:
1) The tune was set to a default that was too lean or too rich. When I did a lot of sequential WOT driving, it would "learn" to adjust, but would forget after a period without WOT.
2) Under high boost, oil was getting past the check-valve into the charge-pipe, which was then messing up the AF mixture and causing detonation.
I replaced the GMR tune with the Trifecta tune last fall. I experienced the detonation once with the new tune. Over the winter I installed an oil catch can and a high-flow cat, and I replaced the check-valve from the charge pipe going into the intake manifold. I haven't been able to reproduce the problem, though I only recently de-winterized and started driving the car again. If I were in your shoes, I'd install an oil catch can and a new check valve. If that doesn't work, try the more expensive option of a new tune.