Your shortcuts should use the switch to specify which mirc.ini file to use (I think it's -r, but I don't use it and can never remember). If you run two or more copies with different scripts/settings, then you need multiple copies of mIRC.ini. Note that using the switch lets you have a single install of mIRC and run it multiple times with different scripts and settings if you want, or you can still have multiple installs.
The alternative to using a switch in the shortcut is to have mIRC.ini in the mIRC install folders and to have separate installs for each copy you want to run. This is what I do so I can easily keep things separate. To do this, just put mIRC.ini in the same folder as mIRC.exe for each install and then set up the scripts/settings as you want for each install and they won't interfere with one another.
The notes about that are in the version history text file somewhere around version 6.35.
