Running the repairDatabase command turns off the database profiler after the repair completes. The repairDatabase command should set the profiling level of the repaired database to be the same as that of the pre-repaired database.

In addition, the repairDatabase command doesn't copy the system.profile collection. repairDatabase is implemented using Cloner(), which does not clone any system.* collections except system.users, system.js and system.indexes. It is is expected behavior for system.profile to be omitted when using Cloner() for initial sync, but it is not expected for system.profile to be omitted when using Cloner() for repairDatabase.