Just noticed that the 2016.5 early version has problems with bouncing clips.
 
I had a number of little groups of short cliplets split off of a long audio clip, and there were some clip gain envelopes there.
 
I tried to bounce a group of cliplets into one clip, but they stayed separate. The first try would bounce some cliplets but others remained unbounced and they would all remain ununified.
 
It was only after 2-4 consecutive bounces I managed to get them bounce all into one clip, but at that stage the volume had changed unevenly within the clip (afaik due to the clip gain automation envelope being applied more than once).
 
Odd. Anyone else noticed this?

Did a quick test. No problem; clip gains applied and all clips merged as expected.
 
I can't see how repeated bouncing would apply gain more than once in any case. Either the bounce succeeds and clip gain is rendered, or it doesn't and the clip gain is still 'live'.
 
How were you selecting - lasso or Ctrl+clicking or...? Had you set the Edit Filter back to Clips? 
 
Final release of 16.05 is out, BTW.