Changing the next track to play during the last few seconds of the currently playing one results in incorrect behaviour. When clearing the playlist, or changing the next track, the song that used to be next plays instead. After this, songs that were added between the old and new but incorrect track are not played.
If you clear the playlist and add a new set of tracks, the after the extra track that shouldn't have been played from the old playlist has finished, the new playlist starts playing from the item numbered consecutively after where the extra one was (instead of from the beginning of the playlist, which is what happens normally).
I have OSX 10.4.11 with the latest software updates, and a powerpc architecture. I am running Version 0.07 (r635) of Cog. This is repeatable with a variety of files and file formats.
I don't expect gapless playback to work reliably during these situations, but this is clearly not the best way to handle it. Specifically, I would expect replacing the entire playlist would cause the new one to start from the beginning after the unwanted track has played. Having silence while the newly set track is loaded would be the best solution.
I hope this helps.