Registration isn't saved in the ini file by default anyway. It's stored in the registry. Reg info is only put in the ini file if you use the -portable or -noreg commandline switches to tell mIRC not to use the registry, so you shouldn't even be having this problem.
FWIW, I would advise against forcing users to use your mirc.ini. Loading scripts is easy, just have a single file that loads all the important files and have the user /load -rs that file in the instructions. Telling a user to install your settings file is far more complicated than doing the above, especially because you're telling users to put the mirc.ini file in the same directory as mirc.exe, which will break any Win Vista+ installation inside of Program Files\
