Most likely. You did mention that it was rather loud right around the time Tyrann was going on one of his BURN, MAIM, KILL sprees during operation: speed run the finale. I figured you would have heard the little ding after I introduced the boss rush to an entire world of pain.
Yargh. A trophy is supposed to pop after the first real dungeon as well. If you end up teaming up with a certain wisecracking book but you saw no pops, then yeah, it's safe to say it's time for a reinstall (so make a save on the roof, that way you could just redo that boss fight.)