Do you have the system configured to import Windows registry data from inventory (like described here: Common: Importing Registry Settings)?
If so, it may be that too much data is being imported in this way and it is causing the reconcile to take a long time to process it all.
The import log should include a message like the following which will give some insight into the volume of data you have:
Found additional 12345 Registry WMI Evidence records in source database
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