Well, obviously, you can overcome this by not booking the same flight numbers when making the reservation...just take a different flight from LAX-IAH and then connect to the flight to Amsterdam you originally wanted to be on...just come in a little earlier.

I just looked LAX-AMS and it gave me multiple options, including the one flight number and others with different flights from IAH...you just picked the one that would screw you out of the miles, unfortunately.

Instead of just 47 all the way through, you could have taken 47 and switched in Houston to 1095 for example for the same base fare price ...just look down that page...

6392 vs 5579 miles for the exact same trip...it's really weird, but clearly displayed nonetheless