I'd like to add another piece of info here.
I am also using the fix and i've found that running the .bat file may not be necessary for making the fix work at least on my computer (laptop).
I had the fix disabled by running the ''uninstall .bat'' and deleted all the relevant files. Then, i re-copied the same files to my SH3 installation and by mistake i forgot to run the .bat file. I only entered the X & Y values. Shortly after i realized that the game was running with no issue even though i hadn't run the .bat file. I'm running Win7 if that makes a difference.
Also, taking screenshots by pressing prtsc doesn't work for me and others too. It results to CTD.