Update on this, (sorry for double post). I never got around to finishing the texture to a good standard, now that Battlezone 98 Redux is coming out, its most likely obsolete anyway, providing they improve infantry/pilot textures.
For some reason with 1.3.6.4z43 the Commander doesn't build the power plant(think that's what shes supposed to build) or the MortorBike Factory. The constructor just stands around.
I've tried restarting the mission and loading a save but the exact issue happens every time.