I just came home, found my own iPad in the same state. So I plugged it in, and upgraded it to the beta 3 ..
After it finished updating, iTunes said "You need to update iTunes to use this iPad" .. So I did. After updating iTunes aswell, when I connect the iPad it just says "There is a problem with your iPad. We're sorry, the iPad you connected may be damaged and can not be activated for service".
I have not registered the UDID of the iPad with the developer account, since it didn't seem to require this for the beta 2 to install - so I don't know if that will change anything. Could this be the issue? That I have to add the device to the developer account so it will verify and activate the account? (Didn't need that to install beta 2 anyway). It's a company account, so I don't want to eat up our device slots if it's not necesarry.