I get exactly the same behaviour with Aperture 2.1.3 on a G5 Mac with an ATI X800 ATI
If I understand correctly you've never run Aperture 2.x before ? Maybe the feature you want was in 1.x (which I never used much) but not in 2.x ? So the issue is Aperture, not the graphics card ?
I'm not entirely sure what "Mirror" is supposed to do that is different from "Alternate", but Alternate does what I want so I've never really got bothered by it.
I'd suggest reading the User Guide - it may be that what you want has been renamed or even removed in 2.x