Good catch! I'd hope this is something to be resolved soon (i.e. carried over to the API), as the new icons seem to be in place since yesterday only or so - at least I recall looking at my accounts tab several times within the last days (including yesterday) and would swear the beta site icons all looked the same back then still.
Either way this is another indication that the respective API entities don't seem to be simply retrieved from the same backend data tiers like the site entities, which, while not surprising and understandable for more complex topics, still isn't exactly a sign of a mature backend architecture either.
Admittedly the Stack Exchange team is moving quite fast in times, making things like this difficult: I'm regularly impressed by their quick turnaround times on bugs (that is, if they take note of them at all in the first place ...) and sometimes multiple daily releases accordingly.