Not seeing a reply to this and it is a little old. not sure you got the answer you were looking for but here is something to look at.
In LDMS 8.8 the Scan and Repair Settings have added the ability to wait for different events before applying a patch. If you look at the Scan and Repair Settings that are being used for the repair task the options for repair are:
Notify user with message
Notify user, also allow cancel
Wait to repair until machine is locked or screen saver is running
Wait to repair until user is logged off
My guess is that your Scan and Repair Setting - Repair tab option is set to one of the "Wait to repair........"