I finally got this figured out. I double checked the Sites and services for both domains and the subnet the computers that have the issues are on were not in the secondary domain. I added the subnet to the secondary and pushed the client, after that the clients were able to find the Site so i was no longer getting the error "Unable to retrieve AD Site Membership.
Then i realized the computers in the second domain for Windows 2003 computers are showing up in Devices as Unapproved. I had to right click and select Approve and that's what fixed my issue. Awesome.......