Well I would call it a bug if a single instance of the IDE reset comm ports other then the single select comm port selected.
That's what it does. I have one sketch open fiddling with one board.
The other board is connected but not being used by any instances of the IDE.
Not sure if it always does this or just on occasion but I think it always does it.
Today it seemed to 'half reset' my board too. The music was still playing from where it was (will only stop when arduino is restarted - as long as the rMP3 has power it will keep playing) but the LCD displaying the visualiser froze. I had to reset the board to get the LCD to start working again.
I will look into it more when I get the chance (and I remember :P)