In the drive-failure panic that made my day a little edgy, I may have solved the problem and bought my self a little more time from the panic. Someone in the Apple forums suggested I open Console and look for clues when I repeated the steps that usually brought up that alert window. Sure enough, something related to Chronos/Soho Notes appeared every time. I safe booted with the shift key down, removed the chronos prefs, repaired permissions again and rebooted again. Whadya know. I think it's gone now.

Thanks again for your help, Jory. You can add this to you expansive knowledge base.

I'm still going to start considering a new iMac before this old tower dies.