Wow. Considering MA2.6 and MA3.0 have barely a line of code in common between them, that IS strange. MA2.6 is built for DirectX 7. MA3 is built for DirectX 8, requiring a complete rewrite.
Could you try downloading the screen saver at
http://www.DreamAquarium.com/ to see if that one gives you the same trouble?
Do you have any other apps you can use to test the 3D abilities of your computer?