This is why I suggested you use the -r switch, which changes mIRC's root directory (ie. $mircdir).
You can set it to anywhere you want by specifying a directory with the -r switch. For example:
mirc.exe -r"C:\Somedirectory\mIRC2"
Note: mIRC will only create at most one new directory so if you set the new config directory to something like -r"C:\Users\Me\[color:red]New Directory\And Another\Blah"[/color] mIRC will fail to create the new directory and default back to the usual location.