"My Itineraries" seems to be showing you the flights the way you booked them to get the extra segments....

In similar cases, Mr. Chicken has given me the BPs to get all the way to my destination (and then some, in some cases). I think you'll be OK.

Otherwise, take what Mr. Chicken gives you, and then somewhere along the way (at the gate maybe), ask an agent to check you in for the rest of your segments (having a Mr. Chicken e-ticket receipt should help you explain your itinerary).

Good luck, and hope you get your 100 EQS ^