Rain soft Q2 no water in brine tank

I have a similar situation that just occured. I had to stop the 1st cycle when I realized the brine tank valve was cracked and if I didn't shut down the system, the tank would overfill. I replaced the valve, set the float, and restarted the system. Thinking it was ok, I left it alone. After a couple of days I went to check on the system and I found the brine tank half full of water. It usually only has a gallon or two at the bottom.
I also found the little white ball that sits in the clear plastic viewer, in the sealed position, (clear plastic viewer was full of water and the ball was at the top) Usually the clear plastic viewer is emtpy and the ball is setting at the bottom.
I tried to trouble shoot this by bypassing the system and relieving the pressure. The viewer emptied and the ball went to the bottom where it's supposed to be. When I repressurized the system, the little viewer filled up with water again and the ball went back to the top.
I then started the cycle to see what would happen, and as you have stated, the tank could not fill with water, because the ball is sealing the opening. Is the system out of phase? There's nothing in the manual for something like this.
One other thing I did was reset the entire timer. I unplugged the unit and removed the back up battery. When I reinstalled all the power, the cams did a 360 full cycle and moved to what I assume is the starting position.
What else can be done?

stage 3 is backwash, no water sucked from the brine tank. 5 is when the brine water is used to clean/regenerate the resin. when the system is giving you soft water, the clear tri-guard in the back should be close to empty and the white ball inside at the bottom. Water will not flow into the brine tank if the tri-guard is full and the ball inside is at the top blocking the flow. Did you happen to remove the tri-guard? There is a little white arrow looking thing called the poppet between tha tri-guard and brass elbow, that prevents water from flowing into the tri-guard, and it sounds like it's not working or missing.

poppet on the bottom of the clear plastic viewer between the brass elbow and the clear plastic viewer is bad or missing, or lines on the clear plastic viewer are reversed.