That sound right. Orbitersim ignores that mass of attached vessels; the UpdateMass function adds the mass of all the attached vessels to the shuttle mass.
The other problem you might have is with the CG updating code. Currently, the CG updating code estimates the ET CG based on the amount of propellant left in the ET tank resource. You'll probably have to change this a little.
Yeah, I changed GetETPropellant() to call the ET and get the prop % in there (I'll look at that in detail later on). That means I'm not considering the mps manifold prop mass in that % calculation, and it's probably right because on a LH2 cutoff the manifold would be full, and in a LOX cutoff the manifold wouldn't be full, but it wouldn't be that far away from that.
BTW any luck with the ATVC angles?