I have a Canoscan 8600f scanner, and it scans film quite nicely. With one problem. I can scan the same film strip several times, and each time the colors are slightly different. I execute calibration and zero out all the bells and whistles in the software, but the colors are still a moving target.
I have the 9950F, but must admit I do not do much color scanning in the classic sense. Most is sepia or selenium toned analog B&W prints scanned in 48 bit color mode.
I do find the colors consistent though if I use the "execute calibration" option in the scan software, even the sometimes very subtle color casts of these partially toned prints.
Are you sure you give all of your machinery enough "warm-up" time? I would recommend switching on all equipment, especially monitor and scanner, at least 1/2 hour before starting to work.
The shifting colors might otherwise be caused by the warming up.
IT-8 calibration might be a good thing, but even in that case, the above warning should be taken in consideration.
Marco