I can only speculate, but I think it has to do with whether it is a "legal" routing or not. It very much depends on what points A and B are. For example, I've flown DAY/CVG/CMH - BOS/PVD about a dozen times in the past year or so. I've NEVER been able to get a routing through MSP (and score more miles); it only allows me to route through DTW. From what I've noticed, from a place like BOS if you travel to the Western destination then you go through MSP or MEM. If you travel to Eastern destinations they usually route you through DTW. Some places give you a choice, while other routings are inflexible. If I wanted to go DAY-MSP-BOS I'd have to do a multicity ticket. Maybe it's one of those cases.

(Again, just speculating...)