Yes, you are being punished by choosing a direct flight and booking it as one segment. There are other reasons you should not book "direct" flights.. your chances of upgrading are also diminished because both segments must have space at the same time for you to clear on either segment.

In the future, NEVER book direct flights. If you need to take 2 flights with the same flight number use the multi-city function and book each segment separately. Then you'll have the appropriate number of coupons for confirmed same day change, and your upgrades can clear individually.

Up until about a year ago for direct flights with a stop you were only awarded miles based on the nonstop mileage but at least this fraud has been corrected and now they give you the correct mileage.

It's been discussed ad-nauseum in this forum..."direct" flights should be outlawed.