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
I bought the upgrade to Ver 2 when it came out instead of buying a new license. Well by "mirror" I mean in full screen mode I get both displays showing full screen and the HUD can float between both displays. Now in full screen mode the secondary display goes blank.
Will go back to check the user guide again. Speaking to Aperture Support they managed to replicate the issue but nothing has come out of it except "we'll pass it along to the software engineers". I would like to have this feature back!