Because, well, they are flairs.
Quite a long time ago, the HTML-based flairs were changed to the pngs, probably to allow them to serve their actual purpose better - be embedded anywhere to show your profile.
However you can still access the old HTML flairs, which appear to have borked styling since they're obsolete and nobody looks after them. Notice that I can't embed it there, SE system strips advanced HTML from the posts, so as done by social networks or etc (except for your site :), where showing off your flair makes sense.
Note that this wasn't directly related to Area 51 though it was affected. Area 51 proposals pages show the user flairs while the site is in the beta, and snapshot flair after the site graduating, to save historical rankings. Since the flairs became pngs, they are shown as ones.
Just noticed: for the sites which were shutdown and no longer exist, the flairs are converted to the html ones. E.g.