I noticed this too, but not with every game. It does it with Metal Gear, or rather, did it with Metal Gear. In this instance, the game seemed to be emulating too slow and you can tell by the music. It was just a tad slower than it should be which caused the audio to slowly and gradually lag behind the video (audio playing too late). It wouldn't get horribly bad, but definitely noticeable. Then all of a sudden, there would be a hiccup in the audio and the sync would be perfect again and would stay that way most of the time.
I found that messing with the emulation speed, then putting it back to default fixed the problem and also makes the game play closer to normal speed. Nestopia still can't handle recording it, though.