Hertz is notorious for this. Almost without exception, every promo I have booked has appeared in the rental contract when I pick-up the car, but is not taken into account by the return agent. I think it is a training issue, namely that the return agents with the portable units have to hit a key(s) to "enact" the promo and they always forget to do so. Whether it is intentional or not, who knows.
I now carry with me a printed copy of the reservation booking showing the final estimated rate (including the promo) as well as a complete copy of the promotion. If the rate the return agent gives me is not the same as the estimated total (or very close at least), I tell him/her it's wrong and that they didn't include the promo. They usually don't have a problem making the adjustment.