messed up reconcile can be caused by a few things but the 2 you may want to check is the load on the mail server, specifically the RPC request/sec and RPC request queue. If the server is having too many RPC requests thrown at it than it can handle, it will simply not service the requests.
Also check if the users have exchange cache mode on; RIM recommend this is turned off
You cannot change the reconcile frequency. It is dependant on the level of activity on the device; it gets batched up and sent to the BES
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