It's mostly the CSM main panel that is the problem. And for some reason it has gotten worse from Orbiter 2010 to 2016. I don't think it's a graphics card problem, but a CPU one instead. And it's also fairly random, sometimes I am getting 60 fps on the main panel then I switch back and forth between panels and suddenly it's only 30fps. And sometimes it can suddenly become 60fps again.
The reason is probably the number of bitmap operations that are going on on the CSM main panel. We have an outdated 2D panel system that only consists of bitmaps, not 2D meshes. And there certainly are lots of performance inefficiencies. We don't really have a proper panel expert in the NASSP development team, but I have just finished a big project for NASSP (the mission control support feature) and I guess I'll tackle this issue and try to find out what is going on. Hopefully I can figure something out soon!