I would try setting the SciTE_HOME environment variable, and also moving the global properties files to the same directory. If that doesn't work, I would try converting the installed version to "portable" by adding a file named $PORTABLE to the same directory as the SciTE executable. I suppose that...

I need to relocate the Profile folder (currently @ My Documents\AutoHotkey\SciTE\). A quick check of the 'properties' files and Registry didn't show anything. In the virtual environment I'm working in it's necessary to use the Installer (vs. Portable) version, but Junctions (Symbolic Links) can't be...