I've only played around with my multiple displays a little and don't really use two, so just some more suggestions.
Have you tried using the Color Management settings in Vista and applying default profiles to each monitor?
Access the "Display Settings" window by right-clicking on the desktop of the PC, left-click on "Personalize", and then select "Display Settings". Select a monitor profile and set it as the default monitor profile by following these simple steps:
1.Click on "Advanced Settings" in the "Display Settings" window.
2.Select the "Color Management" tab.
3.Click on the "Color Management..." button.
4.Make sure that the "Use my settings for this device" is checked.
5.Click on "Add".
6.Select the desired monitor profile from the list.
7.Click "OK".
8.Click on "Set as Default Monitor Profile".
9.Close all windows and reboot the PC. The profile and calibration settings will load at startup.
I don''t know if this idea would work but what about calibrating each monitor individually?
Another calibration software to try
Monitor Calibration Vista - Calibrate your CRT or LCD computer monitor. Calibrate your CRT or LCD computer monitor.
And this thread might be helpful if you run into any problems with profile not loading or restoring
Monitor Calibration Issues - Vista Forums