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