I had the same issue under Workstation 9.0. The Release Notes for Fusion 5.0.2 include the comment "Addressed graphics issues with Autodesk Inventor, Altium Designer and SolidWorks." This sounded promising so I tried Workstation 9.0.1 (although the 9.0.1 Release Notes don't mention Altium). The problem appears to be fixed.
Working configuration: Lenovo W530 with nVidia Quado K2000, Discrete Mode graphics and VT-x enabled in BIOS, Centos 6.3 x86_64, "nox2apic" kernel bootarg, kmod-nvidia (310) and nvidia-x11-drv and nvidia-x11-drv-32bit packages from ELRepo, VMware Workstation 9.0.1, Windows 7 64-bit guest with 3D acceleration enabled, up-to-date Altium Designer.