I'm not sure why this works for some people and then not for others.
All I did was install JKA, then installed the 1.01 patch. From there I got OJP and used the installer to install, and then dragged and dropped the new pk3 stuff and dll files in the folder to overwrite.
The way I start my game is with the icon it put on my desktop that I chose to create at the end of the installer.
That's it. Everything works fine for me, not sure why not for some others.