I believe
@ca1ore hit it already as I was thinking the same thing when I read that. I'm not sure why you have different size plumbing unless this is converted somehow. All lines should be the same size. For example I have 3 drain lines each at 1.5" and 2 return lines both at 1". This way primary, secondary, and emergency are all the same @ 1.5". The return lines are both the same @ 1". Everything is happy and consistent. Also, why is your emergency even running? It shouldn't be in normal day to day operations.
As far as display tank water level something is blocking it. I've seen this in my tank when I was alternating flows between a pair of return pumps. I was trying to get fancy with simulating high and low tides. There was a time when they converged and I ended up draining more than the two returns put back. In any case I would look at:
When was the last time your return pump was cleaned
Anything that may be blocking or reducing flow
Do you really have mixed plumbing, if so can you correct
Any other power heads or water movement pumps that could be kicking on at the time when you notice this
ATO schedule