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So I figured out one of the problems last night, the sqlite.DLL on the server was ~200kb larger than it should have been.

I deleted it and reinstalled the plugin and the one it put back was ~800kb, whereas the previous one was just over 1mb.

So its now syncing at the server too... However I now see new problems.

At the server mptvseries is configured to scan at startup and watch for new files.

Even though I had this disabled at the client it seems to have synced the setting so its turned on.

Also I tried marking a show as watched, then checked the client but it hasn't changed there..

Will try and get some logs tonight.