I've noticed this for well over a year but never bothered to report it because I felt like I was to blame for this, and that no normal person would ever encounter it. I never remove songs from the queue, you see.
Well I've found myself no longer using this function as intended as a result: instead, I'd use it, then press play, then immediately stop again, to assure it doesn't affect me. At which point I might as well just press stop after the next song starts, but I digress.
The issue is, if you have the same song in your queue more than once, closing MusicBee immediately after using Stop After Track will make MusicBee open on the first instance of the track the next time you open it. So if I have a track in queue position 50, 500, and 4103, and I use Stop After Track after listening to it in queue position 4103, then close MusicBee, the next time I open it it will start at that same track but in position 50.
I know this doesn't affect many people, but it is still very much a bug, so I figured I'd report it. Hopefully it isn't too hard to fix it.
3.4.7939 P