I recently ran into a problem with User Profile Synchronization in SharePoint 2010. All properties (except one) were downloaded from Active Directory correctly. However, the manager property was missing for everyone and the domain name of each user is wrong. It turned out that the problem was because the domain NetBIOS name was different from the fully qualified domain name in my deployment. For example, FQDN = ABC.com while NetBIOS name = AbcCorp.
There will be 2 things that you need to do extra in this situation.
Enable NetBIOS Domain Name on the User Profile Service Application
1. Logon to a SharePoint server.
2. Launch SharePoint Management Shell as admin.
3. Run the following commands
<Note down the GUID of the User Profile Service Application>
$service = Get-SpServiceApplication -Identity <Guid of the UPS>
$service.NetBiosDomainNamesEnabled = 1
Grant Replicated Directory Changes permission to the synchronization connection account on the Active Directory Configuration Naming Container
1. This is in addition to the permission on the root domain that you normally have to set up.
2. Launch ADSI edit
3. Right click ADSI Edit (at the root) and choose "Connect to."
4. Under, “Select a well known Naming Context”, select "Configuration" and hit OK.
5. Right click on the Configuration naming container and click Properties.
6. Click on the Security tab. Add the User Profile Synchronization Connection account and grant it Replicate Directory Changes permission. Do not grant it "Replicate Directory Changes All" permission, that will not work.
7. Click OK.
Run a user profile full sync after the above two configurations are completed. The manager property should be populated after the full sync is completed.