rainsoft gold series seems out of synch

I have a rainsoft gold water softener. recently there has been water left in the brine tank, and what I finally found was that upon regeneration the unit sometimes starts on cycle 4 or sometimes 5. I have pressed the "secret Button" and walked the unit thru the cycles. Sometimes it hits them all and sometimes it goes back to its funk. Usually I can cycle a few times and get it to start at cycle 4 with the brine draw and slow rinse for 45 minutes, and the go to cycle 5 for the final 10 minute rinse.

So I will ask the experts...what appears to be the problem? Is the CPU board shot, or are the micro limit switches bad or intermittent? Or I could just change out to a Fleck valve and forget it. I really don't want to deal with Rainsoft as this is an inherited system. Thanks for your input.