ummm, why the continued aversion to using command line switches? I have the following in two desktop shortcuts:
"C:\Program Files\mIRC\mirc.exe" -imircuser2.ini
"C:\Program Files\mIRC\mirc.exe" -imircuser1.ini
In your case, mirc user 1 could be bot, user 2 could be shadowdemon etc.
Admittedly, I have installed over an older version, so my "ini" files are still where I left them ... but this won't make a skerrick of difference.
I have only one installation of mIRC and I run two instances all the time. No conflicts, no confusion. The use of different ini files means I can run both instances with different aliases, remotes etc. No conflicts, no confusion.
Blaming Vista for your unsafe computer habits (especially after Microsoft has finally got around to fixing theirs) is a tad bit unfair.