Are you wearing aetherial gear from dungeons? I seem to have the same issue on MNK where I have exchanged a good portion of my gear for aetherial pieces of much higher ilvl but see no change in my average ilvl. I'm thinking aetherial items may not be reflected in the average or the items/ilvl avg is bugged.

I'd venture a guess and say they aren't counted since realistically the only time ilvl really starts to matter is for end game content and then you won't (or shouldn't) be using aetherial dungeon gear. The implementation of ilvl requirements for content and party finder seem to support this.