[Q]

The problem as far as I know is that in SEV the ships will not attack a planet if there is a troop transport with troops present. That is apparently hard coded.
My solution: I use two fleets in sequence. The first fleet has no troop transporter and has the "damage until all weapons gone" for colonies. This fleet will destroy all ships, bases, fighters and sats present and wipe out all weapon platforms (there might be some collateral damage to the colony). Then the second fleet (which can be only troop transporters in a turn based game but better a mixed fleet in simultaneous game) attacks and will drop the troops.
So far this worked very well for me.