Using two side-by-side desktop monitors, both are Eizo's: the (new) prime monitor is the CG241W (widescreen) model, the side monitor is my old 19" (4:3) Eizo L768
Color calibration using the CG241W CD disc, Ezio Color Navigator pairs correctly with a Spyder 2 calibration device. High-end graphics card connects to both with DVI cables; Nivida Quardo FX1500 card allows dual different monitor-scaling setups (1920 x 1200; 1280 x 1054, and they both display correctly). Windows Vista Ultimate is the Operating System.
Dilemma: Can both be - individually - color calibrated? I can't seem to do it.
All ColorNavigator (new monitor's setup program) "slide over" onto old monitor screen... except the very last one where the Spyder2 is placed over the calibration target; it "slides over" but always "snaps back" to the prime CG241 monitor.
I went through this recently. Apparently a lot of PC cards have only one look-up table so can load only one calibration. But some newer cards can do to. Older software may only take advantage of one, even if two exist. So it apparently depends on both hardware and software.
I too have a dual monitor set up. Most video cards will only handle one profile at a time even if there are two DVI outputs on the card. There are apparently some newer cards that will handle two profiles but I can't tell you which ones will do this. The other option is to run two video cards on your computer each one will handle a profile for the monitor that is attached.