Have a new replica server pointing at an upstream server. Server is configured correctly as a replica, and is pulling updates as you'd expect. All clients are configured using Client-Side Targeting via GPO. No synchronisation failures at all. However, all clients, when checking into the replica, get put into 'Unassigned Computers'. Looking at the client-side WU logs I can see that client-side targeting is working properly (the tier that the servers are getting their GPO from is referenced in the log) and this works on our other downstream replicas.
Both upstream and downstream server are WSUS 3 SP2 with KB2734608 installed.
Have tried deleting machines from both the upstream and downstream servers and seeing if they check in correctly to the replica then - no dice.
I have temporarily removed the DNS entry that points the replica at our windows update url and am using a single client with an entry in localhosts for testing.
Here's the log from a client after running wuauclt /detectnow (and, just for grins, wuauclt /reportnow a couple of minutes later):
2014-01-29 23:06:41:500 776 11dc AU ########### AU: Initializing Automatic Updates ###########
2014-01-29 23:06:41:500 776 11dc AU # WSUS server: http://<windowsupdateurl>
2014-01-29 23:06:41:500 776 11dc AU # Detection frequency: 12
2014-01-29 23:06:41:500 776 11dc AU # Target group: Tier 1
2014-01-29 23:06:41:500 776 11dc AU # Approval type: Scheduled (Policy)
2014-01-29 23:06:41:500 776 11dc AU # Scheduled install day/time: Every day at 11:00
2014-01-29 23:06:41:500 776 11dc AU # Auto-install minor updates: Yes (Policy)
2014-01-29 23:06:41:500 776 11dc AU # Will interact with non-admins (Non-admins are elevated (Policy))
2014-01-29 23:06:41:500 776 11dc AU # Will display featured software notifications (User preference)
2014-01-29 23:06:41:500 776 11dc AU Setting AU scheduled install time to 2014-01-30 11:00:00
2014-01-29 23:06:42:016 776 11dc Report *********** Report: Initializing static reporting data ***********
2014-01-29 23:06:42:016 776 11dc Report * OS Version = 6.1.7601.1.0.196880
2014-01-29 23:06:42:016 776 11dc Report * OS Product Type = 0x00000007
2014-01-29 23:06:42:031 776 11dc Report * Computer Brand = VMware, Inc.
2014-01-29 23:06:42:031 776 11dc Report * Computer Model = VMware Virtual Platform
2014-01-29 23:06:42:031 776 11dc Report * Bios Revision = 6.00
2014-01-29 23:06:42:031 776 11dc Report * Bios Name = PhoenixBIOS 4.0 Release 6.0
2014-01-29 23:06:42:031 776 11dc Report * Bios Release Date = 2011-04-15T00:00:00
2014-01-29 23:06:42:031 776 11dc Report * Locale ID = 2057
2014-01-29 23:06:42:063 776 11dc AU Successfully wrote event for AU health state:0
2014-01-29 23:06:42:063 776 11dc AU Initializing featured updates
2014-01-29 23:06:42:063 776 11dc AU Found 0 cached featured updates
2014-01-29 23:06:42:063 776 11dc AU Successfully wrote event for AU health state:0
2014-01-29 23:06:42:063 776 11dc AU Successfully wrote event for AU health state:0
2014-01-29 23:06:42:063 776 11dc AU AU finished delayed initialization
2014-01-29 23:06:47:063 776 fd8 Report CWERReporter finishing event handling. (00000000)
2014-01-29 23:08:46:626 776 fd8 Report Uploading 2 events using cached cookie, reporting URL = http://<windowsupdateurl>/ReportingWebService/ReportingWebService.asmx
2014-01-29 23:08:51:579 776 fd8 Report Reporter successfully uploaded 2 events.
Am I missing a step here that I took on the other downstream replicas and can't remember? I'm pretty sure I didn't - but it's been a while since I installed a new replica server, so I guess I might have overlooked something...