I've set up a test machine with multiple PCI-e nVidia GF440 Video cards and installed Windows Multipoint Server 2011.
I use the same kind of hardware set up with a BeTwin multiseat solution to create a class lab for Google SketchUp teaching (highly OpenGL dependent) and it works ok.
On the Multipoint Windows test machine the drivers seem to be installed OK but I don´t seem to get any hardware video acceleration. Is this a intrinsic limitation of this solution or am I doing something wrong?
I understand 3D acceleration is not supported with Multipoint Server. There has been a similar question on superuser.com and an observation similar to yours documented at the MS support forum.