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The first time you run CS Repair, it may find a large number of files with incorrect permissions. This could take 5-10 minutes to fix depending on how may files need to be repaired.
While it does this, it may appear to some users that the application is no longer functioning. This is unlikely to be the case and we recommend waiting for the application to finish processing.
In future versions we will make it clearer that processing is still taking place and the application is functioning correctly.