Hot tub jets use the venturi principal to increase nozzle jet pressure.
It's possible something is clogged and there is inadequate air at the intake. Luckily the spa is a year old - it should totally be covered under warranty - most manufacturing defects tend to present themselves within the first year of ownership.
White wires for 120V components (AV) go to Area 1. White wires for 240V components (pumps) go to area 3.
The new board might not have the "Set Up #" pre programmed. Looks to me like it has set up # 7 = 1- 2 speed pump only and that's why pump 2 is not showing on the topside. You need to program it for set up 5. Now Maxx or Vita spa stuff is proprietary so finding info can be hard. You should be able to access the low level programming through the topside. Try and hold light button for 30 seconds and see if anything pops up.