I have the Nvidia shutter glasses and the 120Hz 27 inch monitor with the IR transmitter for them.
i have a similar setup myself. i tried the latest driver set (350.12) because my trusty old driver set (331.82) couldn't detect my new monitor. ED seemed to work ok, but it pretty much borked everything else - firefox and windows mail would either crash or have hung processes on exit, ED's launcher didn't work properly, explorer.exe would hang... and so on.
i tried 341.44 which solved all the other issues, but ED looks a bit strange in spots and the 3D effect is greatly magnified compared to the 350.12 set - i had the intensity almost switched off but it still diverged a bit too much in some parts, like the Vulture canopy bars. some suns look really bloody horrible with a large pattern of dark circles on the most highlighted areas
i'm going to try 347.88, which is the only set left untested between the other two - i hope i get the best of both worlds, a good looking ED and Windows without hangs and freezes. if not, then i'll stick with 341.44 and hope nVidia don't fudge the next release
---> 347.88 works fine for all situations and ED support is quoted as 'Excellent' - but the 3D separation is fairly minor and subtle, unlike with 341.44 - your mileage may vary.