http://forum.cockos.com/showthread.php?t=44121
When you bypass an instrument while it's playing, it doesn't send note off messages, so when you re-enable it there can be stuck notes.
To reproduce:
1. Create a track with a virtual instrument.
2. Set its sustain to full.
3. Insert a MIDI clip in the timeline with some long notes.
4. Start playback with the FX window open.
5. Bypass the instrument while it's on a note.
6. Stop playback.
7. Re-enable the instrument and hear the note still playing.
Expected behaviour:
When you bypass an instrument (or an effect that takes MIDI input, not much of a distinction in Reaper though), Reaper should send a note off message for every note currently playing.
I tried to think of a reason for leaving it this way but couldn't.