I've had the same problem. I've been renting most weekends from my HLE since the beginning of the year, often using the free gas promotion. More than half of the time, they've performed the calculations as you describe above, which ends up minimizing the effect of the CDP discount and forces me to pay tax on "free" gas.
Usually, they adjust the total to get it roughly the same as what I was quoted, but they refused to do so this past week and I had to pay 22% more than I was quoted in my confirmation e-mail. I tried calling the Hertz billing department for clarification, but they just routed me back to the HLE. The person I spoke with at the HLE was going to investigate and get back to me, but hasn't yet.
Anyone else been successful in avoiding this "free gas" tax?