The physics collision mask didn't update when the animation changed in r77 - this was a bug and was fixed. However, there's another bug that whenever the collision mask is updated (e.g. changing the object size or, now in r78, changing the animation frame) then all joints are broken. Sorry, I'll try and get that fixed for the next build :-\ in the mean time don't try to work around it by creating joints more than once, otherwise when it's fixed you'll end up creating multiple joints which will probably break the physics engine.
TBH animating objects with the Physics behavior isn't a good idea, because changing to an animation frame with a different collision mask enables glitches where the object is suddenly stuck inside another one due to the different collision shape.
A good workaround in the mean time might be to use invisible objects with the Physics behavior, which never change animation frame. Then, place your animated objects on top.