My associated accounts on Area 51 are Stack Overflow (935 rep), Game Developers (203 rep) and Area 51 itself (217 rep) but no flair shows up for Game Dev.
Here are pictures:
I have tried refreshing many, many times.
Associated account icons are only displayed for sites where you have more than 200 rep, and this is only checked daily. So if you just went over the 200 rep mark on GameDev today then it should show up on your Area 51 flair tomorrow.