So I have a midi track. I have two instances of the same thing on this track at different times . When I bounce the entire project one of the instances does not end up in the bounced file. It plays fine when I'm listening to the project, just doesn't export. Ideas?

I suppose it could be some corruption in the Project. If you can hear it in playback but not in the Bounce, and if it's the same material as another Region elsewhere in the song, try replacing it with a copy of the Region that does play in the Bounce. You didn't say if there is other material playing along with the Region that doesn't get included in the Bounce. Any chance the Region that doesn't get Bounced is at the end of the song on its own, and the Bounce range [in the Bounce dialog] doesn't include those bars..? And as always, if you haven't already done it, do a hard shutdown/restart -- sometimes mysterious problems are fixed by that.