Yes I don't know how it got to be the default since I never changed it myself. All I did was upgrade from RC to RTM/RTW.
And to check 32-bit vs 64-bit, open Task Manager and look for "iexplore.exe". For 32-bit, it is "iexplore.exe *32", and for 64-bit it is just "iexplore.exe".
I first noticed there was a problem when the tabs appeared to the right of the address bar. I specifically set them to be below the address bar, but it seems that setting isn't propagated to the 64-bit version. So it is easy for me to tell when it is the 32-bit or 64-bit version.
Did anyone try to drag a shortcut to the desktop and launch IE9 from that? Because as I said when launched from the task bar, it is indeed the 32-bit version, but when launched from a desktop shortcut, it is the 64-bit version.