This happens very often. Systems just don't talk to each other in the same dialect. To get preCheck you need to have a Check-in agent adjust your name in the secure flight section and it shouldn't be an issue.

As for the seating, I got stuck behind a very irate family at a B6 gate a few weeks ago and it seems that OTA seat allocations come to B6 as requests only and are not assured. Frustrating but only way to make sure you get your seat is to do so via the airline.