That's pretty bizarre. I am inclined to say that it can't possible have anything to do with VoxCommando, but you never know with computers. There is nothing that I can change in the code, that is for sure. I have always used analog output for my sound on all my computers (until very recently) and this has never happened to me.
If it happens consistently with a particular command then you should edit the command. Try removing the action that puts MM into softmute and see if it fixes the problem. If it does but you can't hear the TTS properly, you can try using MM.pause and MM.play instead. The thing is, the softmute command is simple adjusting the volume of mediamonkey so you may have a deeper issue with MM, or your computer in general.