Yoski, there are multiple switches on the back of the ball count unit.
One controls the playfield solenoids and the other controls the outhole kicker. If I am remembering correctly, the outhole kicker switch should open EARLY on ball 5 (remember, the trough switch advances the unit - not the outhole kicker, so there would not be a possibility for conflict) because even though the ball still needs to be played, the next time the outhole switch will be triggered will be when the game needs to end. I don't remember 100% but I would not only guess but speculate that it SHOULD open early on ball 5.
The only time the unit ever advances without the trough switch (and by the outhole switch) is for game over. This is controlled through a score motor switch. While 1A was the position for a game over relay fix in two of my other games, these more modern games do not have this relay (nor did my Sky Jump, which I am using as reference) - I believe the switch was a different one that I had to adjust personally, even if 1A is relevant to this problem. Do you have the schematic? The different switches will be listed on there as they stopped being listed inside of the cabinet by this point. I know for a fact the switch I adjusted was not 1A and it fixed my problem until the back of the ball count unit started acting up which I then also fixed.