Ok, time for an update on the audio glitch issue...I think I might have figured out what is going on. I think it was a problem with my sound system settings, not the edit!
I tried the AVCHD this time, and still had the same problem. I tried a second time, but this time I put my ear right up to the front left speaker. I could definitely hear music continuously, but the volume was pretty low.
Now, with most action movies, I have to turn the center speaker volume up as far as it will go in order to hear the dialogue over the explosions and gunfire and whatnot. But I have noticed that with DTS sound I don't have to do this - the center seems naturally louder for some reason. And when I popped in the Blu-ray, I saw "DTS" on my system.
I realized that I thought I was hearing a dropout because the center speaker had music as well, and the center was cranked all the way up relative to the R-L speakers. All I was really hearing was the music in the center drop out, which makes sense since the dialogue is cut at those three spots. I dialed back the center volume, and voila - no noticeable dropout anymore!
The only thing I don't quite get is why I didn't hear the problem with the center speaker cranked when I checked the Blu-ray. Anyone have any thoughts on this? Maybe it has something to do with converting retail DTS sound to non-DTS fanedit sound?