I just let fusion upgrade itself to 3.1.3 (416484) on OS X 10.6.98 (10K540). It's on a mini with NVIDIA GeForce 9400 adapter. I've noticed immediately that IE 9 and Outlook 2010 don't repaint the window correctly after a change. IE 9 scrambles portions of the window and the latest Flash add-in has some problems. Outlook just stops repainting and you don't see a correct list of mail items. I suspect there are other symptoms in other programs, has anyone else seen problems?
You might be able to enable 3D accel but just disable Aero (switch to either a 'classic' or simply a non-aero theme) within Windows to achieve the same net effect.
Aero has a bit of overhead, so disabling that might free up the vgpu buffer for what your apps are doing.