Today I booked BDL-SFO in M class and SEA-BDL in A class--web site correctly calculates the 50% bonus in skymiles earned but shows MQMs equal to the miles flown, without the 50% bonus for M class and above.

Also, I first searched each as one ways and saw 15-25 options. Search for them together, either by price or schedule, and most options come up on the outbound but only 8 on the return. It seems random as to which ones show up for the return trip.

Additionally, search based on schedule and it comes up with a more expensive overall fare because the web site won't use the A fare (cheapest on many flights on Aug 2) for the return but uses a considerably more expensive H or M fare.