Because I'm pretty sure I know how to get you past this.
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Ok please do the following as I cannot sit here and wait:
Do you have superuser icon? SetCPU doesnt indicate root. It simply requires it. If it couldnt obtain root permissions then you have to go into super user icon and allow it. Then reauto detect settings. Or simply uninstall setcpu and reinstall as long as you have SU icon. If you dont have SU icon:
DL Terminal Emulator from Market. Type SU. If it says permission denied then you dont have root. So.... you probably have a faulty DL on the Rooter zip. Redownload and try again thru SPR. If that still doesnt work, then we can manually push the SU adb commands however that is more involved and we shouldnt discuss it here. BUT, you have SPR and I KNOW this whole guide works so let us know what happens. CJM knows a lot too.
Shattered,
What happens when you press the su icon in the app drawer?
Swyped from a Droid
Shattered,
If you had root those apps would show in su, therefore I don't think you're rooted. I would go back into recovery, wipe and reflash the update.zip.
Swyped from a Droid