First, try using Motorola One Click Root. I've used the same program for my Droid Pro and it has worked before. If that doesn't work, do the following.
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Warning: SBFing your phone will erase all of your phone's data and applications.
You could try SBFing your phone and rooting again. I don't know if there are any updated SBF files out there, but the one I have always used is the Froyo SBF file, and it works. I think it'll work for you too. I would take these steps:
1) Download the Froyo 2.26.20 Droid Pro SBF file.
2) Download RSD Lite v4.9.
3) Boot your phone into recovery (plug your phone into your computer via USB, then restart your phone. It should come up with a recovery screen.)
4) Open RSD Lite on your computer and your phone should show up on the list. (It may not show your phone's information, that's fine.)
5) Click on your device, open your SBF using the program, and click start. When RSD Lite say it's done, you can unplug your phone and reboot it.
6) Assuming you used the same SBF as I did, you'll be on un-rooted Froyo. Now I recommend you connect to Wi-Fi and update your phone to Gingerbread. (by going into your phone's settings, About phone, and update). There should be 2-3 updates, and it can take a while.
7) Once you're on Gingerbread, go into your phone's settings, Applications, Development, and enable USB debugging. Once you've done that, plug your phone into your computer via USB, and make sure the connection is Charge Only.
8) At this point you can use Motorola One Click Root to root your phone.
