I know the thread is old but I wanted to share a few fixes I had for this game with 3d Vision, as I'm sure a few will replay the game in anticipation for the sequel!
First, windows 7 x64 does not have direct X9 installed by default, so if you are having issues getting GLdirect to work (will get "cannot load open gl subsystem" error, I believe), download and run the direct X9 web installer (google search) and that should get you up an running. The only problem now is the depth is incorrect and the health meter is in the center of the screen, obscuring the view.
A work around for the health meter issue caused by GLdirect is as follows:
First enable the console in the game options
Than use the "~" key to open up the game console while playing
type "ui_hud 0" into the console and the health meter disappears, leaving an unobstructed view.
Unfortunately you will not be able to see your red health meter or the blue meter (forget what that is called), but you can always type "ui_hud 1" in to toggle the HUD again and check, then untoggle it as before.
Also, go to "set keyboard shortcuts" in your Nvidia control panel under "set up stereoscopic 3D," click the drop down for "Hide advanced in-game settings" and check "enable advanced in-game settings." You will see Ctrl + F6 will increase convergence and Ctrl + F5 will decrease. while in the game, without your glasses on (you should see double), hold Ctrl + F6 until alice is not doubled anymore (may take a few seconds), and this will mean she is exactly at screen level, creating a better 3D effect (the game defaults with her very deep into the screen). The issue with this is the cutscenes are now very far out of the screen, so using Ctrl + F5 to move her slightly into the screen still allows for great 3D during gameplay without the headache-inducing pop-out during the cut scenes. Don't forget to work with the depth slider on the emitter as well, and play with these settings until you get what suits your tastes.
Use Ctrl + F7 to save the changes so that you do not have to set this every time.
Also, I'm assuming most people with 3D vision have widescreen monitors, so use this guide to get the proper resolution while playing: http://www.widescreengamingforum.com/forum/viewtopic.php?t=3408
. Remember to run alice.exe as administrator (if you right click -> properties -> compatibility you can make it so it always opens as administrator) so that it can access the .cfg file and load the proper settings.
Took me a while to get this figured out, hope it helps someone! The game is excellent in 3D, with only the glowing power-ups at a slightly-incorrect depth. It is well worth the tweaking to get the proper effect!
<- gldirect (extract the opengl32.dll to the base folder in the alice install)http://www.microsoft.com/downloads/en/details.aspx?familyid=2da43d38-db71-4c1b-bc6a-9b6652cd92a3&displaylang=en
<- directx 9 installer