Does the Hide clock start ticking after the Mark clock has completed or do they run together?
Yes. It's in the user manual and help:
When an aircraft is at the edge of reception cover, sometimes it will not be detected when the screen refresh is due. If the aircraft is not detected, then it will be marked for timeout after the set time expires. The aircraft will still be visible in the aircraft list and on the map until the end of the setting in the 'Seconds to hide timeout flights'.
If you set the timeout to 30 seconds and the hide after timeout to 60 seconds, then the aircraft will be removed from the list and the map after 90 seconds. If the aircraft is detected during this time, then the timeout is canceled until the aircraft fails to be detected and then the process starts again.
