I can't reproduce this problem.
When you're switching between Portable and Non-Portable mode, you are also switching between mirc.ini settings files. It is possible that the mirc.ini that lives in the same directory as your mirc.exe file, used while in Portable mode, has a configuration to hide notices. Or you have a control.ini file in the mirc.exe directory with different /ignore settings.
Download and run "Everything", and type in mirc.ini
to find all of the rogue settings files flittering around your harddrive. You don't have to install "Everything", it can be run portable. https://www.voidtools.com/downloads/