I had a similar situation when I qualified for 2P last year (qualified on Wednesday flight out, had return flight on Sunday). My EQM/EQS posted and my status updated on Thursday, but when I checked in for my Sunday flight I couldn't change to E+ without a fee, was still seating area 4 and OLCI wanted to charge me to check a bag. I'm guessing there's a glitch when you start an itinerary with no status and end it with status that prevents the return leg from updating.

I just printed out a screenshot of my MP account and brought it with me to the airport and went to the 2P counter. The ticket agent was able to change my seat and waive the checked bag fee. You may be able to call the ICC and have them make the changes, but I had no time crunch so it was just easier to handle at the AP.

Definitely make sure you get your status updated for your return flight, the 25% EQM bonus that 2Ps get will add up on your cross-country trip!