This is an old trick so use it at your own risk, but what you need to do
is boot into Vista without any monitors plugged into the graphics card.
Once the windows desktop has loaded plug the primary monitor back in and
windows should start the plug'n'play hardware discovery wizard... the
secret to making the profile stick. Repeat for the other monitor (with
your primary still attached).

Worked, thanks. But I only unplugged the hdtv before starting, and plugged it back in when I logged in. All the modes are back. Clone mode has 1920x1080 again. Single monitor mode has 1920x1440 again. I did one warm reboot and the settings held. The real test is boot after long power off.