Ask for supervisor?
Last week UA posted miles for first and last legs of COS-den-ord-MSY. They didn't post DEN-ORD. All flights taken were those on my original itinerary, i.e., no changes in flights.
Called the 1K desk to ask for the miles to post, they transferred me to Mileage Plus (aka the International Call Center) where the pleasant person wanted me to fax my boarding pass, etc. Said since I was on my originally scheduled flights, and their records show I made the first and last legs of the trip, w/ only an hour between connections, credit should be given for the flights. She repeated the request to fax my boarding pass... Asked for a supervisor, repeated my tale of woe and credit for my DEN-ORD flight was posted as a "one time exception." The flight credit showed up in about 2 minutes.
If you aren't seeing the flight as posted, ask for a supervisor, that should help. If not, it may be important to send in an email request and document your request so if they take months to get this corrected your miles won't be lost due to delay.
Hope this helps.