Came across this issue with a client in which the internal name of the domain was being loaded into User Profiles - as in internal\name instead of domain\name; forgot where I got to a post about this so I am reposting here.
The reason for the issue is that the NetBIOS Domain Names are not imported by default, thus internal\. There is a fix through Powershell however if you have just discovered this, here are some tips:
1) If you have already imported but have just installed, drop the User profile service and recreate - the change below MUST BE DONE BEFORE YOU IMPORT!
2) If My Sites are active, you cannot do drop the UPS so you that so you will to rely on running the full import a few times to get it right (I've had difficulties with this working everytime)
Login to the server running Central Administration using the SharePoint Farm Account then go to Start > All Programs > Microsoft SharePoint 2010 Products > SharePoint 2010 Management Shell - when the Powershell window opens, enter in the following command:
(List of Service Applications and their Id's (GUIDS))
Locate the User Profile Service and copy the GUID under the Id column then enter:
$UPA = Get-SPServiceApplication –Id <GUID of User Profile Service Application>
When done, return to Central Administration/User Profile Service and start the import, all should be well.