Thanks Rad for reporting that. In fact it is a known issue, and you correctly identified the cause - a long MG stop sound. The TCB doesn't know anything about the stop sound, not how long it is or even that there is one. When you tell the TCB to stop the MG it thinks it happens right away. The TCB is controlling the light so it stops the light, but the sound card is controlling the sound and it keeps going. You can re-start the MG on the TCB and the TCB will happily start blinking the light again, but the sound card says "Wait! You aren't done with the stop sound. I will not comply."
The most direct fix is the thumb fix. The user, knowing he loaded a long stop sound, needs to restrain his thumb from re-starting the MG right away before the stop sound has completed. Also this is a very good example why it is important to eliminate any silence at the end of your sound files, and fade them out very quickly.
Another fix which I will consider is that we instruct the user, when using the OP Sound Card, to move the MG light from the TCB output to one of the outputs on the Sound Card. Your early prototype doesn't have any light outputs but as you know the current version has 3. Since the Sound Card knows how long the stop sound is, it can more accurately control the light output, preventing it fro restarting while the stop sound is still playing.
However even that wouldn't be 100% perfect because the TCB could still be firing the MG IR signal at the wrong times. The perfect fix is either for the user to specify in OP Config the length of their stop sound, so now the TCB is aware of it (which is more work for the user and more settings to clutter OP Config); or most ideally of all have the Sound Card communicate via serial to the TCB on startup this kind of information. That's the best solution but is also the more time-consuming one, and considering only a handful of people in the universe even have one of these devices, I am probably going to postpone it until such a day as they become more widely available.
But thanks for bringing it up and reminding me, I will add it to my long-term to-do list.