Had something strange happen.
Running Sapphire 1.0, installed stock ROM, then incognito. Everything was working fine. I know that phone and contacts were working this morning. But tonight, when I tried to launch them from LauncherPro or the stock launcher, I got "could not launch the requested application". And, both apps were missing from the app drawer.
The only thing of significance I had done since this morning was to run zipalign_apk this afternoon.
Reboots did not bring the phone back. I tried running 'switchapk phone stock', but it still did not work. Fortunately I had backed up the ROM yesterday. I restored it, and everything is working fine. I restored the backups of the few apps that had been updated since the backup, and it's still fine.