Hi Ofer,
These are benign warnings and should not affect the speed of your repair process.
The warnings here are related to the elapsed timer which is normally started when mongod starts listening for incoming connections.
Since you are running mongod --repair, mongod will run the repair command to completion without starting to listen for incoming connections (so the elapsed time will always be 0ms). You'll see these warnings emitted periodically during the index build stage of the repair process as internal stats are updated; the warnings should ideally be suppressed in this context.
Regards,
Stephen