md5sum was the same for two downloads (ae51529b980bf671b4440f5acbf52f2f Supreme_Sense_v9.1_a2sd.zip for anyone searching - it isn't posted anywhere that I saw) so I assumed the md5 was good, clearing it all out and reflashing from scrach fixed it until I restored my apps from Titanium Backup.
It turns out that the personalize menu is linked to the Sense launcher and I had set ADW as my default launcher.
So if anyone runs into this again, all you need to do is go to Manage Apps, and clear the default from your chosen launcher, then when you go to Settings -> Personalize, it will prompt you whether to use Sense or your other launcher. Choose Sense, make your changes, then hit home and re-set your other launcher as default.
This allowed me to customize my lockscreen apps (gmail instead of mail, handcent instead of messaging, etc.), and continue to use ADW as my launcher after.
---------- Post added at 11:18 AM ---------- Previous post was at 11:13 AM ----------
Any thoughts on why Root Explorer can't mount /system as R/W unless I first mount it R/W in MikTweaks? Is that by design?