I had sort-of the same issue last month when I flew LAX-HND, booked on UA, but operated by ANA. Tried all the name combination to log into ANA website and it kept saying something like "unable to display reservation". Called ANA, and they said because my itinerary was code-share with UA. They only had middle seats at the time, but was able to assign me a seat.

At 24 hours before departure though, I was able to log into ANA's website and check-in as well as choose an exit row seat.
Ended up not matter though, they upgraded me to Premium Economy at the counter in LAX when I drop off my luggage...