I have tested the 4/21/16 patch, and rug stacking is now fixed for lots when placed via build mode. However, it is still bugged for saved rooms and lots placed via Manage Worlds (place option; the place and edit option is okay). I recommend keeping this issue open until the problem is completely resolved.
Edit: more detail regarding saved rooms and rug stacking. The saved room will look correct in your library, but when you place it on a lot, you will in all likelihood see the rugs out of order. If you hover the room over different positions on the lot prior to placement, you can actually see the stack order change as you move it around (somewhat fascinating to watch). If you are working with the lot where you originally designed the room and can recall exactly where you had the room positioned, when you place the room in that same spot, the rugs should be stacked in their proper order. This suggests to me that rug placement is currently linked to their position on the lot.
However, it's worth noting that if you stack some rugs in a room on your lot and then pick up that room to move it elsewhere on the lot, while you will see the same effect as you move the room around as if it were a room from your library, the rugs will take on their proper stack order once you place it. Likewise, if you fixed the stacked rugs in your saved room after you have placed it on the lot and pick it up to move it to another location, it will appear that the order is goofed up again, but once you place it, it's fine.
