You can disable it by opening the script editor and in the Options menu, click '
Monitor File Changes'
This is happening because although you're running two separate mirc instances, they're most likely sharing the same settings folder ($mircdir) and settings file ($mircini) which you could find out by typing the following in both...
//echo -a $mircdir | echo -a $mircini
You can make one of them use it's own settings file by closing mIRC and create a txt file in that mIRC folder and name it mirc.ini and then start mirc. Note that after you do this it will be a clean install and all settings for this copy will be reset to default. The settings for the other copy however, will still be there as it will still be using the old settings file.
Also, read the following from
versions.txt, which is what you're experiencing...
16/08/2007 - mIRC v6.3
Changes:
..
20. For Vista compatibility, new installations of mIRC now save all
settings in the User's "Application Data\mIRC" folder by default.
However, if the installer or mIRC find mirc.ini in the same folder
as mirc.exe they will use the mirc.exe folder for all settings.
Users installing over an old version of mIRC should therefore see
no change in behaviour.
The installer is now also aware of administrator and standard user
accounts and installs mIRC accordingly.