Just another similar (although different) data point:
I've had a similar thing occur with Hertz where I was using my corporate CDP from two employers ago. It turned out that the contract with Hertz allowed for earning miles on only two preferred airline carriers and not the one I wanted to get miles on. Normal rentals would be fine, but the daily rate was a few bucks higher so I opted to use the employer CDP. I guess this was done to 'encourage' employees to divert business to the airline partners. (UAL & AS)
I called and talked to a number of reps and while they clearly admitted that I wouldn't have any way of knowing this info ahead of time, it's in the CDP# contract and there was nothing they could do. I was hoping to get a token "we're sorry for your misunderstanding" mileage credit, but in this case I got nothing.