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?

First thing to look at would be the Start & End locations in the Bounce dialog box -- check to see if the Region that's not ending up in the bounced file is maybe outside this range (those locations will pick up the range of the Cycle ruler if it's active)..