I've had that happen only a handful of times and we fly with Southwest all the time. We typically have two reservations: one for my husband and I and another for my father and mother-in-law and sometimes my sister-in-law. Sometimes we do this because we have found a certain fare is only available for a certain number of seats in one reservation and other times it's because of the payment method we want.
What seems to be happening more often is people paying the extra amount for a pre-check-in where the system will automatically check you in so you don't have to stalk the website exactly 24 hours prior to your flight time. This might be causing what people may describe as random boarding positions because in theory you've got real live people checking in 24 hours prior to flight time but you also have a software program doing the same thing at the same time. Theortically this could make people in the same reservation not have the boarding positions in numerical order.
A couple years ago we used to get more middle to end A's nowadays it's usually B's (never a C though because we do it 24hours exactly) and usually our flight is mostly to fully booked everytime we fly even a couple of years ago.
My husband has been traveling back and forth from home to Houston every two weekends since July until Christmas and he does the pre-check-in (as it is for business and his company pays for it). He always gets an A but sometimes he gets towards the end of A (he's told me that it doesn't appear that many business class people are on the flight most times meaning more people have done the pre-check-in).
This is just my thoughts though