I had problems with a metamorph theme for handcent, in which you had to move the apk file from data/apps to system/apps in order to apply the theme. The theme caused issues with Handcent so when I tried to uninstall, I had to do it manually through root explorer. Even after I deleted the apk, it still showed up in the dockbar, but not in my app drawer. I could still open it up. It took me awhile to figure out how to get it off, but persistence, and a good internet connection revealed many smart people and good tips.
Sent from my Raptor Ally using DroidForums App