The pegasus I'm using t o replace the Walker's Lliberty criuser in mission 11 and the Cylonbasestar replaces the nomad battle ships in mission 13.
I can get both of the ships to show up and have created loadouts for them, and in the case of basestar modified the solararch entry for it.
The problems I'm having is that the ships aren't firing any weapons and when I scan them they aren't showing up or on the models.
However the pegasus can still move foward(its engines work). and on the basestar the weapons can be seen on the model and when you destory it the weapons are dropped as loot.
To complicate things even more if I replace the omaha at the end of mission 11 with the basestar it can uses the weapons and fires at you.