Stop doing the doroot batch file and do it by hand. Open the batch file and send the adb commands one at a time, or follow the adb droid x root ota 2.2(droid 2 method).
Environment variables and pathing can make the batch file falsely finish and say you are rooted.
Follow this guide for the commands. If you did not set your environment path variable, dump everything into your adb directory.
http://www.droidforums.net/forum/droid-x-hacks/82584-droid-2-root-dx-ota-2-2-a.html
btw: you can paste into a command shell to make it very easy to do it manual
Click on the upper left icon on the command shell window, referred to as the system menu, and along with Move, Size, and so on, you'll see a sub menu called Edit. Click on that, and you'll find Copy, Paste and other clipboard related commands.
What he said ^
dont trust batch scripts, to many variables. copy/paste is your friend though, take your time in ADB, wait for the prompt to change, also make sure your device has USB debug (look for the icon in the notification bar, if its not there, it wont work)
and remember... take your time!