I just ran LAX MSP ANC MSP LAX and I had some glitches with the app. When I checked in for LAX - ANC it also checked me in for MSP - LAX on the return, despite being outside of 24 hours (I showed up on the UG list and the app showed "checked in".
I was not however checked into ANC - MSP, so when I boarded I got the red flash and the agent had to do something before I could board, I'm guessing check me in. I didn't lose my upgrade though, thankfully.