Did you extend the AD schema?
If you have configured the Boundaries. Please make sure that the AD site boundaries groups are set as "Use this boundary group for site assignment".
1.In the Configuration Manager console, click Administration.
2.In the Administration workspace, expand Hierarchy Configuration, and click Boundary Groups.
3.Select the boundary group you want to modify.
4.On the Home tab, in the Properties group, click Properties.
5.In the Properties dialog box for the boundary group, select the General tab to modify the boundaries that are members of this boundary group:
To add boundaries, click Add, select the check box for one or more boundaries, and click OK.
To remove boundaries, select the boundary and click Remove.
6.Select the References tab to modify the site assignment and associated site system server configuration:
To enable this boundary group for use by clients for site assignment, select the check box for Use this boundary group for site assignment, and then select a site from the Assigned site dropdown box.