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WSUS Replica Server Fails on Synchronization - hangs at 99%

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I'm hoping someone out there can help me because I'm about ready to tear my hair out.

I had configured a downstream server as a Replica and it worked fine, synched fine and distributed the updates no problem.  Unfortunately the disk ran out of space and I had to move the Content folder.  Since then it's all gone to hell.

Both Servers are Windows 2003 SP2, both using Windows Internal Database.  I've removed WSUS completely from the downstream server and reinstalled from scratch but the problem persists.  Downloads are copied into the correct folders but when it gets to 99% it hangs and then fails.  In the SoftwareDistribution.log it was showing the error in datastore SQL Timeout error but I've noticed having removed everything and reinstalled that the SUSDB.mdf and SUSDB_log.ldf files have different Date Last Modified times.  They were updating fine during the Initial Synchronization but at some point the log file stopped updating even though the database file continued to grow. 

I've checked the access permissions on the database and folders and everything is as it should be, I've checked everything in relation to KB2720211 and all the issues therin but at the moment I haven't even bothered installing in on the Replica server.  I've checked the configuration of both WSUS installations and they are the same, they are both set to use Group Policy and the Computer groups etc have all been synched but the point at which it's failing seems to be the moment where the Approvals etc are supposed to be synched.  The SoftwareDistribution.log file also claims to have a Date Last Modified date which is correct but appears truncated.

Caveats here are that the database files are on the D drive and the Content Folder is on the E drive and the E drive is an external USB drive but it's a 7.5K drive so it shouldn't be a problem.  There are roughly 40GB of update files and the Database on the main server is about 5GB where the Replica is about 2GB.  The Replica is also a DC.

Am I missing some simple gotcha?  Some daft setting?  I'm all but convinced that the problem is because it's on an external drive even though I can't find anything to suggest that it's not supported.


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