First off, let me say that User Profile Service is provisioned and generally runs normally. We're running on February 2012 CU.
We're in the middle of a domain merge, combining five AD domains into one. During the run-up to this, we would periodically have issues where some users in the destination domain would have their profiles overwritten such that the Preferred Name field just shows their account name. Example - Company User, logging in as MY_WEIRD_DOMAIN\user, will come to work and log onto SharePoint to suddenly find documents created by MY_WEIRD_DOMAIN\user instead of Company User.
It's not happening to everyone in the domain at once, only a few people every so often. The ones it does happen to, however, always show the NETBIOS domain name (MY_WEIRD_DOMAIN) instead of its DNS equivalent, notasweird.com.
It doesn't appear to be a temporally-sensitive anomaly either. Of the six accounts currently showing NETBIOS instead of DNS, one is less than six months old, while another is about four or five years old. Three of them are accounts that were created for users migrated to the domain (me being one of them), and none from the same originating domain.
The destination AD forest has a 2003 and two 2008 servers, and then we have a local R2 in our office that the forest replicates to so that we don't need to go over WAN. Could the non-homogeneous environment be the cause for this? If so, is there any way I can work around it short of decommissioning the old DCs? I'd love to do that but it's not my turf.