You are correct in thinking that games should be capped at 60fps Vsynced in 3D mode - the most you will ever see on a 120Hz monitor on active shutter glasses is 60fps in each eye no matter what the framerate is being reported as. If it is capping you at 30fps then it seems to be reverting to a 60Hz operating mde under 3D which is a little strange. There are two possibilities:
1) You don't have it connected up with a DVI Dual Link. You did say you get 120Hz on the desktop but are you sure of this - do you ever see 120fps when gaming in 2D using Vsync and the lowest settings?
2) Your GPU is not very powerful. I know you don't need to be told this but it is a bit of a mismatch for such an expensive and capable monitor and given the rest of your system. Operating under the TriDef 3D mode reduces the frame rate to less than half of the original value due to the additional processing and splitting of the frames into each eye individually. I am sure you are aware of this though because you have been lowering settings massively to see if you can increase it above 30 and it seems that the 30fps is a definite cap. I'm not sure if this is what is happening but it is as if the monitor refuses to run in 120Hz under 3D on your GPU. I have a S27A750D running on a 6950 with a 60fps cap as you would expect - have you tried updating the Catalyst drivers as well?
1) Yes it is 100% Dual Link DVI. I checked the model number on the cable on samsungparts.com (as it is the official supplied cable with the monitor) and it checks out. Also under display settings i have 120hz refresh options in 1080p (not available if its not displayport or dual link dvi) and using fraps easily get vsync at 120fps in games such as WoW and TF2, Portal, etc. Also using fraps at the desktop i get 120fps when moving windows around rapidly.
2) Yes i agree it is a weak point of my system, however as i mentioned and like you said, i have turned the settings down to a point where im getting almost 200fps in 2D (over that in TF2 and Portal when settings turned down) yet as soon as i enable vysnc in 3D it caps at 30fps. If i was getting 60-70fps in 2D then yeah i would chalk it up to low GPU power (which is exactly what i thought at first, until i noticed it happening on less GPU intensive games).
Also, when not using vysnc in 3D in WoW i was getting 80fps. As soon as i enabled vysnc, 30fps. So it could definitely power 60fps.
The problem now is, every game i start is capped at 30fps regardless of vsync settings. I have it turned off in the game, and also forced off in my Ati control centre. Yet now when i start WoW, which at first ran at 80fps in 3D, it is capped at 30fps no matter what i do. Same with every other game.
I have uninstalled my drivers, used driver sweeper, reinstalled my drivers. Same with the Syncmaster Tridef 3D Drivers. Hasn't helped.
These problems are only in 3D when launching with Tridef software, if i loads my games as normal in 2D, vsync settings work as they should and i see locked 120fps in the games where my hardware can manage it.
Edit: Also, the monitor has an information menu on the OSD which tells you what res and hz it is running at, even when i am capped at 30fps the monitor still shows "1920x1080 @ 120hz". So it hasn't really resorted to a 60hz mode. Something is just getting messed up somewhere and thinking it has.
Now is the time to upgrade the monitor from a CRT, I was never a fan of flatscreens before because they were all 60 or 75hz and just sucked compared to CRT's but this not only has great performance for games it's also very accurate for colours much like sRGB mode on the 997MB CRT.
Very impressed, worth the money imo.
I think the monitor must be allergic to the GPU or something as I can't see what else could be preventing proper 3D operation. I don't really know what to do about this though.