An update, a week later: Syncing is turned off, and I'm starting to see corrupted and deleted entries on the iMac, but I'm also seeing multiple copies of some contacts on the iPhone. Weird.
Mail also listed an email from my brother as being from a friend of my wife's, who had no email address in the file. It seems the links are somehow botched up.
I'm thinking maybe I should ditch the Mail/Address Book package and go with something else. What else do folks recommend that will sync to the iphone?