Windows 2003 - Active Directory is rebuilding indices

I have installed SP1 and restarted the server and after that it came up with a Active Directory is Rebuilding continuous message. It was on the screen for atleast 20 minutes. The server event came up and I can restart the services manually. I have tested on workstations and remote access. Logons are working and drives are mapping as well. But DNS is short and I do have another DNS server in house. Can anyone tell me how to get this to working. Bot the servers in house are DCs. The server that is having the issue has the FSMO roles.