So, every file changed during the Rootcheck scan should be checked just after Rootcheck ends, but events aren't being lost.
The setting <auto_ignore> doesn't work for that. This option must be at the manager (not the agent) and, when set to yes, makes it to discard any modified file event if that file has been changed more that 3 times, so files that change too often won't trigger an alert.
Best regards,
Victor.