Thanks everyone for the help. No matter what I do today, I can't get Calibre to recreate what in the world was happening yesterday.

Today everything is co-operating no matter what I do. If it happens again, I'll repost with a debug log, but for now everything is back to normal. I'm sure it will happen again at some point because this kind of stuff happens to me all the time.
Maybe Calibre is just chuffed that I posted here and decided "Now that you have posted to MobileRead I'll be good".
Again everyone