I think that this might be a bug in InDesign but I thought that it might be handy to know.
Here's how to recreate: Create a rectangle 200px x 200px, with a 4pt stroke. Set Align stroke to INSIDE. Set the top left xy pos of the rectangle to 100px,100px so that you can easily see changes, and leave the Reference Point in the top left. Now when you change stroke widths, everything is fine, and change corner types, everything is fine, EXCEPT the Fancy Corners. So if you choose Fancy Corners, the x/y becomes 96,96 and total width/height changes to 208 x 208 which is incorrect. Now change the Align Stroke to "OUTSIDE", and the x/y changes back to 100,100 and the rectangle size changes back to 200 x 200. Completely backwards, but just for the Fancy Corners.
Please comment if this is an expected response.