If you are having issues with vista forgetting what your desktop monitor configurations were with 3 monitors on 2 cards.  Please try this

Tested with nVidia Driver version 186.18 and Vista x86 w/ SP2

 1) Open the nVidia Control Panel.

2) Navigate to Display -> Set up multiple displays.

3) Uncheck all monitors except your primary monitor.

4) Set the resolution to what you want.

5) Close the nVidia Control Panel.

6) Open the Administrator Services Window

7) Find the "NVIDIA Display Driver Service" and open the Property Sheet.

8) Set the Startup type to Disabled, click Stop, click OK.

9) Reboot

10) Open the nVidia Control Panel.

11) Check the boxes for your monitors, set the resolutions, click Apply.

12) Close the nVidia Control Panel.

13) Open the Windows Display Control Panel.

14) Position the monitors how you want them.

15) Click OK and Close the Windows Display Control Panel.