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I am using merge replication with SQL 2012.

When performing a clean sync using the merge agent I am getting a timeout on this stored procedure,

sp_mssetupbelongs

I am wondering what the best way to diagnose this issue? When I take the SQL that was run, and run it in management studio it runs instantly. I can only assume that part of the required operations were done the first time it was run and timed out.

More specifically it must be a particular group of merge articles that are slowing it down, so how can I isolate this?

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Have you looked through this: msdn.microsoft.com/en-us/library/aa937532(v=sql.80).aspx? I know this is for SQL 2000, but since this stored procedure has been around since then I doubt troubleshooting it changed much with SQL 2012. –  Shawn Melton Nov 26 '12 at 2:00
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