I know this thread is old but I had the same problem today, that Red Alert 3 would only run from the integrated graphics instead of the Nvidia card, so just in case someone else have this problem too.
The problem is that the 3D profile settings in Nvidia expects the file "ra3_1.12.game" to end with .exe, but it does not. So to fix it I used the Geforce 3D Profile Manager (http://www.geeks3d.com/20100528/manage-your-sli-profiles-with-nvidia-geforce-sli-profile-tool/) to import a txt file with the settings, then changed a line in the profile that looks like this:
Profile "Command and Conquer: Red Alert 3"
ShowOn GeForce
ProfileType Application
Executable "ra3_1.10.game.exe"
Executable "ra3_1.5.game.exe"
Executable "ra3_1.11.game.exe"
Executable "ra3_1.8.game.exe"
Executable "ra3_1.12.game.exe"
Executable "ra3_1.2.game.exe"
Executable "a3_1.7.game.exe"
Executable "ra3_1.0.game.exe"
Executable "ra3_1.7.game.exe"
Executable "ra3_1.4.game.exe"
Executable "ra3_1.9.game.exe"
Executable "ra3_1.3.game.exe"
Executable "ra3_version.game.exe"
Executable "ra3game.dat.exe"
Executable "ra3_1.1.game.exe"
Executable "ra3_1.6.game.exe"
Executable "ra3.exe"
Setting ID_0x00d55f7d = 0x20000000
Setting ID_0x1033cec1 = 0x00000003
Setting ID_0x1033dcd2 = 0x00000004
Setting ID_0x106d5cff = 0x00000000
Setting ID_0x1095def8 = 0x02800205
Setting ID_0x10f9dc81 = 0x00000011
Setting ID_0x10f9dc84 = 0x00000200
EndProfile
To this:
Profile "Command and Conquer: Red Alert 3"
ShowOn GeForce
ProfileType Application
Executable "ra3_1.10.game.exe"
Executable "ra3_1.5.game.exe"
Executable "ra3_1.11.game.exe"
Executable "ra3_1.8.game.exe"
Executable "ra3_1.12.game"
Executable "ra3_1.2.game.exe"
Executable "a3_1.7.game.exe"
Executable "ra3_1.0.game.exe"
Executable "ra3_1.7.game.exe"
Executable "ra3_1.4.game.exe"
Executable "ra3_1.9.game.exe"
Executable "ra3_1.3.game.exe"
Executable "ra3_version.game.exe"
Executable "ra3game.dat.exe"
Executable "ra3_1.1.game.exe"
Executable "ra3_1.6.game.exe"
Executable "ra3.exe"
Setting ID_0x00d55f7d = 0x20000000
Setting ID_0x1033cec1 = 0x00000003
Setting ID_0x1033dcd2 = 0x00000004
Setting ID_0x106d5cff = 0x00000000
Setting ID_0x1095def8 = 0x02800205
Setting ID_0x10f9dc81 = 0x00000011
Setting ID_0x10f9dc84 = 0x00000200
EndProfile
Simply changed from "Executable "ra3_1.12.game.exe" to "Executable "ra3_1.12.game". Then imported the modified txt file again with Geforce 3D profile manager.