So I am wondering increasingly if my other issue, Cross vCenter vMotion fails, is due to an underlying issue with the PSCs as I can find no issue with the code (or other peoples code).
Currently have two vCenters in seperate physical sites. Each site has an external PSC. Logins to vCenter are handled by placing both these PSCs behind a netscaler load balancer. Our "DR" side is the primary PSC in the pair with the local one to me being the "secondary".
I logged in to the "DR" PSC and checked the replication partners using vcdrepadmin:
./vdcrepadmin -f showpartners -h drpsc1.domain.com -u administrator -w [password]
ldap://invmumpsc1.domain.com <------ Being decommissioned
If I run it against the other PSC listed above I get:
./vdcrepadmin -f showpartners -h invpsc1.domain.com -u administrator -w [password]
Vdcrepadmin failed. Error [Server down] 
I am unsure though if this is an error because the other PSC is secondary when setup behind a load balancer or if we do actually have a PSC replication issue. I have tried rebooting the invpsc1 VM but the same result is returned. Anyone using load balanced PSCs able to confirm what output they get from the vdcrepadmin commands?
UPDATE: So did some digging around the PSC and a lot of the logs files stop about a month ago. Ran some checks on services and the bulk are in a stopped state. Looks like a failure we had a month ago (snapshot consolidation after backup killed the VM) has also corrupted the PSC. Am awaiting VMware to investigate the cause but think I can just deploy a new one and follow the same KB to deploy behind a load balancer but just running the scripts on the secondary node. Anyone had to do this before?
Message was edited by: Tim Alexander - updated status
So got clarification from VMware that replication should be up behind the load balancer and all services should be running. Looks like a failed backup had caused the issue but further then that cannot work it out. The bulk of the services on the appliance had ended up with chkconfig being set to "off" so reboots would not bring the services online.
Started the services manually, changed the chkconfig back to on for the appropriate run levels and now everything is synced across the two PSCs.