I have figured out how to regulate my LQ. First of all sealing the air leak at my vac-alert with plumbers putty did the trick to stop the air from entering the system. As air infiltrated into the LQ's lines with each days pump start up is was changing the flow rate. Now that there is not an air leak the flow rate stays the same. I also noticed that I attached my flow meter higher than the top of the LQ tank, to make it easier to read, so I lowered it because I noticed that air was being trapped above the ball on the flow meter. These were the 2 changes that I made to my system and it has corrected the problem.
I contacted Brian from vac-alert and asked why the unit is leaking air and he said a 2HP pump is too much for my 20,000 gallon pool, so now I don't know what to do get a smaller pump, get a new vac-alert, or just leave everything alone and hope that in an emergency my vac-alert will work. I have dual drains, but I also have 2 small children. Any thoughts?