A little background will help here.
We have multiple DC's across multiple sites, site 1 (head office) has two DC's - DCSite1-001 and DCSite1-002, our branch offices all have a single DC and are connected to Head Office via a full MPLS network. The site links are great, all ping communications are done typically under 1ms.
I have a problem between our main site main DC (DCSite1-001) and one of the remote site DC's (DCSite2-001). All of the other sites DC's can replicate to and from the main site DC, it is only these two machines that have a problem. DCSite2-001 can replicate with DCSite1-002, just not DCSite1-001. Again - all other servers in other sites can replicate fine with DCSite1-001.
I have checked the obvious like time syncs, updates etc but everything looks ok. I have run PortQuery and it gets stuck when connecting from DCSite2-001 to DCSite1-001 using TCP over port 389. The problem i have is this server can connect to another server in site 1, just not the main DC. Servers in other sites can connect to the main DC so it can't be that the port is blocked on the server.