Playback sounds fine but when I bounce to audio it clips extensively - how to solve?

There are several possibilities, but one of the most common is that some of your source tracks output is routed directly to you soundcard's output ports, while other source tracks are routed properly through the master bus you set-up for the mixdown.
 
If that's the case, the bus's meters will indicate that you are well below clipping, and the mix will sound fine, but when you bounce the entire project down, the tracks routed directly to the soundcard's outputs summed with the master bus that the rest of the tracks are routed through will cause clipping.
 
The solution is to be certain ALL of your source tracks are routed to the master bus (or to a bus that is in turn routed to the master), so that the master bus's meters accurately reflect the total mix's volume.
 

That was exactly it!  Thank you geniuses.  
 
One small follow up question - I have put a lot of volume envelop automation in these long tracks.  When I switch it from the interface to the Master which will be the only thing going to the interface, the levels are quite low.  Is there a way to change the overall volume of the track once the volume envelope is used?