I tried something like this back in, well, either Entrenchment or Diplomacy, I forget which. As I recall I had to tinker with 'random' planets a bit more to make them work. What excately it was I can't remember, its been too long ago now.
Similar to Seleuceia's question above, are you using in-game maps, map designer maps, or galaxy forge maps?
Let me compound the issue by asking this: Do you run any other mods (other than Real Cap Ships)? What I'm thinking of is 7 Deadly Sins, or anything that would have custom planetary bonuses that effect starbase/tac/log slots at a planets. Perhaps its one of those 'overwriting' your mod.
You did mention that you modified the Real Cap Ships mod. Perhaps Real Cap Ships isn't affecting these planets for some reason. Try making your own mod for the 2 SBs at each planet, and running them side-by-side.
And when in doubt, play VL, they're above the need for defending planets after all.
EDIT: Heading off the grammar police...