Some user preferences lost

My brand-new Mac Mini was fine last night as of midnight. Sometime today, many but not all of my user preferences/software registration settings were lost. Eudora will not open, with an error message in the console log, Couldn't reopen address book databsse. Home directory may not be ready or is missing.
The home directory is still therre, as are all my files; in the directory I reach using cd ~. I did not rename my home directory. Obviously relevant, I can only see 3 accounts (including my usual account) in the log-in window. The folders are in the users directory on the hard drive, and they look normal in every way I can tell. NetInfo manager shows the accounts there, however.
All login items (chronosync, USB overdrive,etc) are missing from
I have VMware Fusion on the machine, and there are error messages that it could not enter super-mode.
Looking at the permissions on my home folder, the owner is show as "unknown". Since (thank God) I was using an administrator account, I changed the owner to myself.
But what on aerth might have happened? Where could the other two accounts have gone? I'd be most grateful for a pointer in the right direction!

I did repair permission, but I gather that that only fixes permissions for installed items, not user folders. At any rate, it didn't help. I checked the disk with Disk Utility, and Disk Warrior 4 ( which found the usual minor issues, not nothing useful).
Having retaken control of my home folder, now I'm concerned with what happened. There was nothing I could find in the logs to indicate what happened. I had the mini connected to the monitor through an Iogear DVI KVM, and when the computer woke up, it had to redetect the display. I would hope that couldn't cause permissions for the home folder to be lost; but I've connected the mini directly to the monitor for now.

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