The CTRL+F3/F4 won't turn it off... I have the .dll in my LOADR folder, too, and my ff7_opengl.cfg file has
# Load Multiple DLLs
load_library = Multi.dll
Even in Bootleg config options, I see that I had the Toggle option checked off.
Ugh, so annoyed. I just want to play
EDIT: I changed the Multi.dll line to read FF7AlwaysRunKranmer.dll instead so at least I could try just that out. It made CTRL+F3 disable my autorun, as I noticed immediately; I even got a popup confirmation and could see the change in-game. However, I then ran over to the fall-down-the-tracks part again and... same thing happened. I tried on both places you can fall down, too -- same exact issue as originally described, even with autorun off.