I've done some more testing last night and I believe I was able to find the culprit here.
The issue seems to be related to the fact that you have "Run as administrator" on your main package.
I am afraid, however, that this issue might not be related to Advanced Installer, but to the OS.
Even if you do not have the "Run as administrator" option enabled from the "Install Parameters" page and you run the setup elevated (e.g. right click on the EXE --> "Run as administrator"), the same will happen. Considering this is happening outside of Advanced Installer as well (when manually running the setup elevated), I am afraid that this issue is not related to our option, but to the fact itself that the setup is run elevated from the start.
Unfortunately, I can not really say what's the reasoning behind this.