Only to find out weeks later that things still look crazy.. like users from one domain are coming across with 2 different domain names. or that users who started out with one domain name have now switched to a different domain name and now perhaps their MySite link doesn't work any more?
It was only through a call to MS Support that I found out that
If you've already created your AD connections before you set NetBIOSDomainNamesEnabled, you MUST delete & recreate your AD connections.
This was not documented anywhere on technet. The reference the MS Support person gave me was hidden this MSDN blog:
http://blogs.msdn.com/b/russmax/archive/2010/03/20/sharepoint-2010-provisioning-user-profile-synchronization.aspx
So, to repeat, if your Domain NETBIOS name is different from the FQDN of the domain...
1. Delete your AD Connections
2. Set NetBIOSDomainNamesEnabled to true using Powershell
$upa = Get-SPServiceApplication | where {$_.TypeName -eq "User Profile Service Application"}
$upa.NetBiosDomainNamesEnabled = $true
$upa.Update()
3. Reset IIS & restart OWSTimer just to be safe
4. Recreate AD Connection(s)
5. Run Full import at least twice
6. Run incremental sync to get colleagues re-populated
If you are in the same situation I was in where your could NOT just delete connections b/c users had uploaded pictures and profile info these are some scripts that I used to save off and restore the data.
Export User Profile Properties
Export Colleagues
Add Colleagues