I'm leaning toward user error or CA really messed this up.

Taxpayer paid quarterly estimated in April & June.

These two payments happen to match new coupons that I sent to taxpayer the day or two before the payments were taken out of the account and the same day that the state return was accepted. 

I have combed through everything I can think of and there is nothing on my end that indicates AWD, not even for amount due with return.

I also know that taxpayer paid amount due with return on the CA website. Wondering if they may have just made those payments as well and didn't document it - unusual but possible, I suppose.