Auto-enter amounts higher than bill due amount

I'm having an issue where I want to have bills I set up to be automatically withdrawn from my checking account to various bills. As an example, I have a car payment with a monthly payment of $50 (obviously made up). I typically pay more than the payment due amount, say $75 here on a monthly basis. Over time, I become a month ahead and the auto-entry, created on a manual bill reminder and set to autoenter, that used to work, now does not. In the case where I am over a month ahead, I still pay the same amount and I want it to post automatically, regardless of what the bill amount calls for. This seems to have changed with a recent upgrade, but I have not been able to find a cause, have deleted and re-added, and no dice. Scary when I'm expecting that to be accounted for automatically and then just happen to notice there was no entry when reconciling. Anyone experience similar and run into this? It's driving me nuts...