Recently I flashed Cyanogenmod on my HTC Inc after making a backup in ClockWork Mod. I really prefer HTC Sense over Cyanogenmod's and Android 2.3's vanilla UIs, so I was going to restore back to my backup I made earlier. Unfortunately, my battery died soon before I was going to do that, so I recharged it to full while it was off. I tried to boot into CM for one final goodbye, but I got stuck in a boot loop, even though everything worked fine before.
So I decided to immediately restore to my backup. When I did this everything seemed fine at first, until I rebooted. It seems that it restored all my apps, but my homescreen seems to be in the same configuration it was about 4 months ago, and about half of my apps force close right when I open them. I realized that the homescreen config was actually a saved scene that it restored to, and not my previous, unsaved theme.
I tried to use ClockworkMod's "Fix Filesystem Permissions" utility in hopes that CM had changed file modes on my sdcard and that this would fix it, but every time I tried it, it returned with an error that read something like
Error when attempting to run privileged commands, even though the Superuser app granted it root access.
So I tried restoring and re-restoring and wiping data then restoring, all to no avail. What went wrong and what can I do?