I used to use a GeForce 6600 with my Huey Pro monitor calibrator and Viewsonic VP930 flat screen, it had no problems at all, at least as far as the procedure went. I don't think the issue is with your GFX card, especially if you had no problems with this card and calibrator on a CRT.
I would check that you haven't got the monitor set to a fixed set of "sRGB" default settings which then don't allow the calibrator software adjust any settings. I have found that no matter how much I twiddle the settings on my flat screen display, it simply isn't as accurate, nor does it have the dynamic range or subtlety of shades of greyscale as my CRT.
Duncan
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