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The checkout and checkin dialog boxes progress counter applies a one second wait for each feature class, table or relationship class processed prior to refreshing the progress. If the checkout has many datasets and classes, this adds additional time to the process.
Additional time is required to allow the updating of the dialog boxes display for the current status.
Use the checkout or checkin geoprocessing tools to accomplish the same task. The geoprocessing tools progress dialog boxes do not apply a wait time.
Another option is to use ArcObjects.