I use several different scripts (in several different folders) and when I upgrade mirc I install it to a clean folder and copy the executable file to each folder instead of installing to each one. I have done this for several upgrades, and have never had the problems you are experiencing.
Basically, what I'm trying to say, is the mirc.exe does not open files in another folder unless you (or the .ini file in it's folder) tell it to.