First time playing Final Fantasy VII on PC, had it sitting in my inventory for awhile but never got around to actually trying it. I started out by running the launcher and configuring, then I quit out and used one of the torrents available on this site to set up the game as I wanted through BFE.exe. I then launched the game, and realized that the controls are awful on my 360 controller by default, so I installed Pinnacle for the first time in years and downloaded a Final Fantasy VII profile.
If I launch FF7_Launcher.exe, Pinnacle alters the inputs exactly as I had hoped, sticks have analog walk/run, start is on my start button, etc.... Note that Pinnacle is a.) Set to listen for FF7.exe itself, not the launcher. b.) launching the profile as persistent, and c.) mapped keys are sent to any other applications as well when they're focused, such as Chrome.
If I launch Bootloader.exe, none of the Pinnacle mapped controls take effect and everything is based on the original control scheme. Worse yet attempts to change the input configuration through FF7_Launcher.exe don't take effect when launching through Bootloader.exe.
Is this something to do with the Steam to 1998 conversion that automatically took place? Do I have to choose between decent controls and hooves-for-hands unless I go buy the older version of the game instead?