Just as an update:
My JAN 2017 build needed updated software for the DDM and PDM. My dad's MAY 2017 build did not need them, and never had the window issue. Sometime between JAN and MAY 2017 was when the revision came out solving the problem. Mine was revision P, and my dad had revision R (which is the current latest even using IDS 114.03). I did not need new modules.
* 2017 Fusion Sport, 12.7 @ 108 mph tune-only (early tune of mine, bad trans settings), full trunk w/ lunch, and dirty paper air filter
* 2014 SHO non-PP, 12.4 @ 111 mph tune-only, all day long with dirty paper air filter and worn out 30k RS-As