I am also having the same issue with variations only I noticed something extra:
I had 2 attributes and when setting the variations I left one of them set to the "ANY [ATTRIBUTE]" option by mistake and saved the settings.
I then noticed it and went back and changed that variation to the specific attribute I wanted and saved again.
I then noticed that the variation which I originally set correctly had been reset to "ANY [ATTRIBUTE]" but that now the 2nd variation was correct.
It created a loop where each time I tried to change one it would set the other variation to "ANY [ATTRIBUTE]".
In order to fix this I had to set both variations to "ANY [ATTRIBUTE]" then save the changes, then reset each variation to the specific attribute and save the changes
Finally it worked, but so ridiculously frustrating!
Hope the release a fix soon coz this is doing my head in :-/