Timeouts are a real pain, and I was helping someone debug their problems and found this useful info, its from Andy on the SQL Server newsgroups:
A couple of other possibilities worth checking.
In Object Explorer right click on the SQL Server 2005 instance select Properties. I am assuming that you may be attempting to connect remotely.
On the Connections tab check the value of Remote_query timeout.
On the Advanced tab check the value of Remote Login Timeout.
Hope this helps!
Reed
