I can see the same behavior. Don't have an explanation for it.
If it walks like a duck and talks like a duck
Hi Guys -- thanks for your confirmations. I am pretty sure that this is a bug.
There's another interesting facet to all of this too which plays into the inverted function of the stroke alignment when using Fancy Corners... To replicate - if you start with the same rectangle (make sure it is square) as previously described in the same position (top left = 100,100) and turn OFF Constrain Proportions and change to stroke align to center. Change JUST the width or the height, and it works okay. Now undo that change (back to square) and change the stroke align to outside or inside. When you now change JUST one dimension (the width or the height) you'll notice that the other dimension is ALSO changed in the opposite direction of the size change that you just made, and the amount of that change is the width of the stroke. It shouldn't be changing the second dimension at all, but it does, and in the inverse direction of your change of the other dimension.
I'll just sit back and wait for Adobe to be SO thankful for me picking up this errant behavior that they will probably rush to upgrade my CS6 Master Collection to CC for free, don't you think? :-)