I'll bet that some portion of Disk Utility is somehow, erroneously using files from the OS X partition you're trying to repair -- I remember this being an issue when people had Panther and Jaguar installed on the same hard drive on different partitions. Launching programs from Jaguar's Applications folder would cause the application from the Panther partition's Applications folder to launch instead, causing problems.
You mention that you have two partitions that have OS X installed -- when you run Disk Utility, are you selecting a partition to repair, or are you selecting the actual hard drive listed as a parent to the partitions? if you select the hard drive, and not a single partition, then Disk Utility must try an unmount all partitions that belong to that hard drive, which isn't possible, because Disk Utility is trying to unmount the partition you're currently booted from -- it can't do that.
What happens if you do this: Quit all running programs and unmount the partition that you want to repair (just click on it and eject it from a Finder window or the Desktop, like a you would a CD). Then, launch Disk Utility from the OS X partition that you're currently booted from. Next, in the sidebar where the volumes and hard drives are, select the partition (not the hard drive) you just unmounted, and try to repair it. Let us know what happens.