I have a Canon 9000F. Sometimes I use the Canon scanning software, and sometimes I use VueScan. VueScan can be downloaded for a trial and only costs $40 to buy.
Last summer I was scanning some odd film sizes (larger than 35mm) that were sometimes 70 or 80 years old. The Canon scanner worked well for these, since they wouldn't fit in my Minolta DiMAGE Scan Elite II film scanner.
I can't remember for sure whether I ended up using Canon or VueScan software for those. One idea is to start with VueScan, and then work your way back to the Canon software if you'd rather use it.
Now that I think of it, I had to use advanced mode in the Canon software before I could set some of the preferences. It was a bit awkward to find at first. You should be able to scan at 9600 dpi when scanning film - even MF.
Try some Google searches as well as the Canon web site. Here's a pretty good article on the 9000F:
Scanner Review: CanoScan 9000F
From that article:
Preferences. Some of the power of ScanGear is hidden in the Preferences. The Scan panel, for example, enables 48/16-bit output (otherwise the scanner converts from 48-bit to 24-bit color and 16-bit to 8-bit grayscale). It also enables image scans up to 4.0-GB in Advanced Mode but disabling backlight correction.
I believe your problem is the same one I originally ran into - it won't allow higher resolution scans on larger film sizes like MF because the files become to big, unless you use Advanced Mode and set the preferences correctly (which then enables files up to 4GB in size!).
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