The timer resets ONLY if the attacking team in round 1 gets the core. The timer becomes your "clear time" because obviously if they got it one second later than your team. Game is over. So they just trim the 7:30 in a down to however long it took for the first attacking time to dowload the core.
You probably don't know this because you haven't seen many cores downloaded. But next time watch how much time people start with. I have seen buggy voidstars where it randomly throws out a victor. But what you are describing is the map working as intended.
So the team that capped the core first loses and the other team that doesn't even get to download the core wins? How is that working as intended?