I just checked and not all of Bottom Guns planets were based. The planet Dewired attacked DEFINATELY wasn't based.
Combat Start:
Attacker DeWired Beams: 0, Fighters: 4379, Shields: 0, Torps: 4379. Armor: 4379
Shield Tech: 15 , Armor Tech: 15 , Torp Tech: 15 , Beam Tech: 15 , Computer Tech: 15
Defender Planet Beams=0, Fighters: 0, Shields: 43, Torps: 0. Armor: 0
Shield Tech: 11 , Armor Tech: 8 , Torp Tech: 6 , Beam Tech: 0 , Computer Tech: 2 , Base Factor: 0
Notice the Base Factor is 0. If it was a based planet it would be 2. Apparently the planet was attacked and taken by Bottom Gun and never rebased after taking it. I bet the same was true of the other planets.
BTW, you still have a planet in that sector that is not based.