So far I've been able to get both versions to run fine on vista x64, though my computers are setup in an unusual way for regular home user. First major difference is that my computer is part of a domain. That server is running 2003 rc2 x64, though one aspect that may make a difference is that my user is setup as an enterprise administrator; which gives the all access pass and don't get nearly as many annoying security pop ups/problems as the user logged on has administrative rights above the regular administrator.
Additionally the version I installed was a DD from Ubisoft (cd was in my laptop when it got stolen so just bought it over the web); which I'd heard had some extra stuff added to make it more compatible with Vista. This
is not confirmed, just remember seeing it elsewhere (can't recall where), but both GWX and vanilla install and ultimately work fine.