When an activation group is used in Vizzy (in an if() for ex) but no part on the craft uses that AG, it will not show up in the list of AG's during flight.
1) The two side interstages are using AG 1&2
2) Launch, see that AGs are listed correctly
3) Return to the designer, delete interstages, and re-launch. See that no activation groups are listed
The AGs still function correctly in the Vizzy program, they are just not displayed
It's not actually possible to know all AGs used by Vizzy because of that darn halting problem, so what I've done as a compromise is to show all AGs that have an assigned name, even if they are unused, when a Vizzy program is present. So, now you can just enter a name for each AG that you want to show up in the flight scene's activation group panel when using a Vizzy program.