I must have assumed that since Eyefinity was supposed to be natively supported by newer versions that I had a version problem and immediately stopped searching for my actual problem. I can't believe I hadn't found this simple fix before this. I ended up getting it to work just now by altering the GamerProfile.xml file in Documents/My Games/Far Cry 2 directory. The Eyefinity works in other applications etc, so I don't think that's the issue.
The fact remains that the resolutions don't show up as an option. The attached image should show what I'm talking about. I was basing my previous assertions on the properties window of the. I hadn't noticed this before and mine indeed does say v1.03 in-game. You can see the version in top left of the main menu. Gowor: I just checked, and our version was patched to 1.03.