Crock, I had the same issue with my phone. I had rooted it previously... flashed CM7, didn't like, then flashed back to my GB Nandroid. IT WAS NOT ROOTED even though I had superuser in my app drawer. It took an hour, but I got it working again.. On the Droid 3 One Click Root
site it says
If you are trying to root from the OTA Gingerbread update and you were previously rooted, you will probably experience problems with this root method because of the pre-existence of busybox and superuser.apk.
Here's what I did..
1. Get to a windows computer.
2. As mentioned by Byakuskhiki above, use the Droid 3 ADB root method
here by logging in to the phone using "adb shell" and type the following commands:
mv /data/local/12m /data/local/12m.bak
ln -s /data /data/local/12m
Next, physically reboot the device by pressing the power button. When it wakes up, log in using “adb shell” again, and type the following:
rm /data/local/12m
mv /data/local/12m.bak /data/local/12m
mv /data/local.prop /data/local.prop.bak
echo "ro.sys.atvc_allow_netmon_usb=0" > /data/local.prop
echo "ro.sys.atvc_allow_netmon_ih=0" >> /data/local.prop
echo "ro.sys.atvc_allow_res_core=0" >> /data/local.prop
echo "ro.sys.atvc_allow_res_panic=0" >> /data/local.prop
echo "ro.sys.atvc_allow_all_adb=1" >> /data/local.prop
echo "ro.sys.atvc_allow_all_core=0" >> /data/local.prop
echo "ro.sys.atvc_allow_efem=0" >> /data/local.prop
echo "ro.sys.atvc_allow_bp_log=0" >> /data/local.prop
echo "ro.sys.atvc_allow_ap_mot_log=0" >> /data/local.prop
3. Reboot your phone, and log in to "adb shell" again. You should get a "#" prompt. Type in
mount -o remount,rw /dev/block/system /system
rm /system/bin/su
rm /system/xbin/su
4. Reboot yet again.
5. Now, download the correct Windows (XP or Vista or 7) One click root package from
Pete's Motorola Root Tools and run it.
Be patient. It took a while for me, but I finally re-rooted my phone.
