So, I tried (and failed) to use Ninjamorph to edit my Framework-res.apk to switch out some battery icons and subsequently had to restore my nandroid backup.
However, both SetCPU and Terminal Emulator came up as "not installed on your phone".
I thought at first that it was because they were on the SD card, but I looked at others that were installed there and they didn't have a problem.
I was able to uninstall SetCPU and reinstall from the market, but Terminal emulator shows up as installed, even though the apk is no longer there.
Any ideas on what's going on?