This happened when I first tried to update to the newest Froyo. I had to use the Droid2 root method to get it all back. All my programs were there (including superuser) but I could use any of them that needed root.
if you lost root then thats the cause. I have found that I sometimes have to rebootstrap though. Have you tried pressing bootsrap recovery then reboot recovery in the DX Bootstrap app?
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