This very same thing happened to me on JetBlue last year after purchasing a ticket through the Ultimate Rewards portal (and providing my KTN. My reservation didn't show up in my Trueblue profile on jetblue.com (and I tried to associate it but no luck). I was able to check in online using my confirmation number. When I received my boarding pass without pre-check, I called JetBlue to see what was going on. The person I got on the phone was very helpful and explained to me the same thing about how my first/middle name came in to their system as one long name. He asked if it was ok if he could uncheck me in, fixed something on his end and then had me checkin online again while he was still on the phone. When I checked in the second time, problem solved, boarding pass came through with True Blue # and Pre Check.

This is the only ticket I booked through Chase Ultimate Rewards so far and it has made me fearful of trying to buy more tickets on other airlines through them.

Funny enough on Delta when I book through my corporate site, my first/middle name always show up when I get my boarding pass but I always am able to see my reservations on the Delta app and have no problem getting Pre Check. When I book directly with Delta myself though, my first and middle name show up as two distinct names.