Already tried logging in as root, no joy. Also ran fsck in Single user mode (much faster boot, btw) and while it found plenty of orphaned nodes, it did not fix the problem. Permissions all seem correct as well.
Oops. I found the problem; I had moved my Mail app to a sub folder of Applications, and X.1 just put the new one in the Applications folder, rather than seeking out the old version and replacing it. So the new one works, but the old one was what was giving me problems.