Upon beaming down to the Vega Colony, my Avatar did not immediately appear, but my entire Ship! (Screen Capture available). Once I moved my avatar the ship converted into the expected "bipedal humanoid" or Vulcan Avatar.
I had the same issue when doing the "Hide & Seek" mission in the Lackey system. I beamed down to the Klingon listening post as my ship. I beamed out and when I showed up in the sector map and was walking around as my ground avatar in Sector Space! I could only fix it by relogging, which with the state of the servers today, of course, meant it took forever.
So the expected behavior for the Avatar was present, but the graphic refresh hadn't occurred until it seemed to detect I/O from the mouse. I wonder if this is just "lag" of sorts?
They are working on a patch that should be out later today (I believe) that will prevent the problem with ships loading on interior/ground surfaces and characters loading in space. It happened to me as well