That's bizarre, I can usually alternate between running and walking pretty consistently...perhaps some kind of setup-particular bug? Use a stock 1.02 ff7.exe to get through that part, then switch back after you save it.
Alternatively, you can always creep along...
Hold walk, take a 1 sec step, let go, repeat, until you're out of the room.
I'll play through that part of my game and see if it happens to me....is it always like that or just for the part at Aerith's house?