OK, I see what's happening.
As I mentioned before, gapless albums now play fine and regular tracks *with another track to follow in the playlist or in the queue* play fine, as well. It's only when you play a single track or the last track in a playlist / album that the problem is seen. I have "Update Track Position in iTunes" turned on, and at -0:05 seconds, you can see the current track stop tracking and it skips to the next track, but the current track continues playing (like the sound is buffered and BitPerfect is reading ahead but continuing to play the current track). If you're on the last track of an album / playlist, however, tracking still stops at -0:05 but the sounds stops, too :/ So any content recorded in the last 5 seconds of the track just disappears, e.g., echo / fade, "ambiance" or even music, if it runs into the last 5 seconds of the track. This does *not* happen in iTunes with BitPerfect turned off (iTunes 10.3.1).
I can also confirm BitPerfect sometimes loses track of the current output device. I have a USB DAC / headphone amp I sometimes use with my MacBook Pro. Sometimes, the sound will stop coming out of the DAC and begin coming out of the internal speakers. If I look at the preferences, I see it's switched to "Built-In Output".
Thanks for doing those extra tests, that's making more sense, I'm pretty sure I know where the problem is now with the tracks getting cut off. As for losing track of the output device, that's a new one, I'm really not sure what's going on there.