Just bought this printer and had the same problem as SpreadHead. I was able to get it working by temporarily changing the printer size to some other value than A4 or Letter, and then changing it back to Letter. When I went back to the 2-sided option, waaalaaa, it was no longer grayed out.
I know this is an old thread, but I thought I'd mention that this solved the issue for me.
I'm running Mac OS X 10.7.2 with a Canon PIXMA MX870 (driver version 10.51.2.0).
My problem is that sometimes when trying to print PDFs (in both Preview and Adobe Reader), certain options in the print dialog are grayed out and therefore not selectable. I am able to check the "Duplex Printing" box, but the "Print Area" subsection below is completely grayed out, and since it defaults to "Use reduced printing" instead of "Use normal-size printing," printing double-sided is impossible, unless for some reason I want everything to print extremely tiny (why IS "Use reduced printing" the default duplex setting, anyway??? Even when nothing is grayed out, I have to manually tell it NOT to print everything super tiny every damn time I need to print double-sided, which is pretty much every time I print!). Likewise, when trying to select the print quality, only "Standard" and "Custom" are selectable; both "High" and "Fast" are grayed out.
If anybody else encounters this problem, the solution that worked for me is as described by JohnnyVmac above -- change to a different paper size, and then change back to US Letter. Magically the selections are no longer grayed out. This is clearly a bug in the driver, but the fix is quite easy.
Hope this helps somebody.