It looks like I’m having a problem with the shell root.
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Use this temporary solution (which utilizes SuperOneClick), until I can get a chance to fix things.

1. Download SuperOneClick from shortfuse’s site: http://www.shortfuse.org/
2. Download my temp script, and unpack
3. Unpackage and run SuperOneClick
4. Boot the Atrix into FastBoot, and enable Early USB enumeration
5. When you see “Reading ODM fuse: 1″, plug your phone into the computer and run Shell Root with SuperOneClick
6. Once rooted, run the temp script “Run Me – Atrix Soft Brick No Root”

Your phone will boot into Android, and then reboot. Leave things alone until that reboot happens, and you no longer have the blinking red light.

Download:
http://www.dangdeals.com/atrix/Atrix…over-noroot.7z

Sorry ’bout this, I hope to get my original script fixed asap.

More @ http://forum.xda-developers.com/showthread.php?t=982859