How often is it happening? Mine may reboot once a month or something but not on a regular basis. Did you ever factory restore your phone because of your battery issues? If this is happening often I would bet you have something gone rouge or something got corrupted.
I'm not sure how you could contact them, but I do know that moto gets a notification each time your phone resets and they could help you i.d. the problem maybe.
Mine never rebooted or froze even once since the first day i got it.... and its been more than two months already... so try to do the factory reset first see if that'll fix it... and if not, you can contact Motorola tech support from their site... the Atrix is covered with one year warranty... ( you can also check that on moto site by entering imei number)
As I know some people had problems with their Atrix after 30 days and ATT sent them refurbs.. So just FYI here is a chat that I just had with a motorola tech rep: http://imageshack.us/f/571/chatv.jpg/ (sorry the image didn't appear in this post so i pasted direct link.....)
It could be an app you installed (or combination of apps) , you should check what you have installed lately
I've recently installed WhatsApp in my MileStone , but it was interfering with both RealPlayer beta & Google Maps (even though I don't start them , they start all together even when i kill one of them) which caused my phone to reboot at least 10 times a day & kill the battery in 1 hour , but when I uninstalled RealPlayer everything went back to normal
Interestingly it has happened twice to me as well. Just roughly 2 weeks ago. It happened twice within the same week. I've had my Atrix since the February release. I thought it might be related to the latest software update but I have no basis for that. I had installed a particular application immediately before it occurred. So what I've done is removed that application. One reboot came with that application running the other after its removal. Not many facts I know ... but I'm investigating.