I think that is just a flaw in the design/mold. The black part that the treads/platform shoes slide onto has some interference with the center piece and won't lay flat even with the treads/shoes not attached.
There are a couple of simpler fixes, but getting it perfect would likely mean some exploratory surgery on that black piece to shave off a little bit from whatever is causing the interference.
The lazy fix is to put the shuttle on the launchpad and stand a deluxe on the grey platform, that should keep it flat. (To highlight my laziness I didn't bother transforming Astrotrain or Exhaust for the photo.)
The other, longer term option without cutting is just transforming it enough times so that it isn't as drastic. Mine now hovers closer to the ground than it originally did and I've probably only transformed it 10-15 times.