I find using midi in my pro tools sessions with instrument tracks really can affect the audio quality. One of the worst plugin offenders is virtual drum instrument BFD3. It hogs cpu and this combined with others knocks about 10 per cent off the audio quality. When you're happy with the midi performance, I would suggest just recording the audio and disabling the instrument. Will make a difference to the end result and you can always keep recording if you change your mind about the drums or other instruments.