What I don't get is why these installation scripts never acted up like this in OS 3.9.
Eeer, change 3.9 to 2.0 in that statement and I can agree. By the time 3.9 came around I very often would have problems with install scripts, even with commercial software.
You also have to remember MorphOS 2.5 is what, 11 years newer than OS3.9? And really OS3.9 is just a bunch of patches for OS3.1, which is about 16+ years old? In PC terms that would be like trying to run Windows 3.11 era software on Windows 7.