I have noticed oddness in Carrara's alpha channels for a while -- definitely since C5P.  I find, though, that the alpha channel is still there, but it's not accessible in Photoshop.  I have taken the animations into After Effects and have been able to use them just fine.  If you don't happen to have AE, it's more problematic.

Out of curiosity, what were your render settings?  Did you have "premultiply" selected?  It sounds like your description of the file as viewed in photoshop indeed is premultiplied.  Maybe C6 has changed how it handles premultiplied alphas, but I've always checked premultiply in my renders because it makes for cleaner composites (in my experience).

When next I'm in front of Carrara, I'll run a couple tests and see if it's a premultiply issue.  I seem to recall that there was a plug in available for Photoshop called unmult; unfortunately the version I found with a quick google search (http://www.redgiantsoftware.com/unmult.html) doesn't seem to do what I recall, which was to extract the alpha from a premultiplied file.  You might give it a try.

Let me know if that works.