We noticed the same thing too last night. For at least one user, the gravatars in chat were not what they're supposed to be on main, even though the profile pages contained the original gravatars (when loaded by the same chat user), what they should've been.
Looking into the issue, I found myself that my Area 51 gravatars are inconsistent:
Now here's the catch: both icons in the above image point to the same gravatar hash, only with different pixel sizes. It's not strictly reproducible (the user who had the issue in chat didn't see the same effect), but for me, here are two gravatar identicons of the same hash with different pixel sizes:
Note that the only difference in URLs is the pixel size; and note that you may not see the same difference. For the record, the top/small one is the proper identicon I should have on Area 51 (if I'm not mistaken, Area 51 uses an unsalted hash from your e-mail, which is why it's different from main).
The above indicates that this is an issue on the side of gravatar; and the fact that it's user-dependent makes it more fun. I blame caching.
Update: after three weeks, both my Area 51 gravatar and my main site gravatar have changed to the "new" one, at every pixel setting, on both my home and work network. I gave up and set my old avatar manually. The bug seems to be spreading steadily, so I'll reiterate my hypothesis I noted in a comment:
Considering that some people are entirely missing their old gravatars, and that for others the old gravatars are only available at specific sizes (those that were used someplace on SE), I have a new hypothesis. What if gravatar messed up/changed their identicon generating algorithm, and the only reason the old ones are around is due to caching? This would explain why only a few sizes are kept as old, and new (hitherto-unused) sizes are generated anew, changing in the process. As I use chat a lot, my avatar is cached there; others who don't, might have their avatar lost with higher probability.
Now that weeks have passed, any caching that kept the old identicons around is gone, and we're left with the old ones. If I'm right, gradually every identicon should change everywhere (unless the user manually sets the old one, of course).