You need to use a "fresh" sh3.exe for it. If ou have an .exe that has already been patched with one of the earlier fixes then it won't work for this one.
But: Maybe the old fix copied your old sh3.exe to "sh3.old". Just rename that one and use it with the new fix.
Or - if you don't want to install SH3 all over again - check this thread for another way to get an .exe that will work:
http://www.subsim.com/radioroom/showthread.php?t=160118