Hi, I have now analyzed the logs and come to an conclusion. The problem is the config line:
This is not compatible at all with AmigaOS 4.1, and this causes the boot problem in FS-UAE. If you remove this line, you automatically get a Picasso IV graphics card (default for the A4000/OS4 model).
The reason it works when started with FS-UAE Launcher is that it (for some internal reasons) explicitly sets graphics_card = picassoiv-z3 when it loads fs-uae with an A4000/OS4 model. This option then "wins" over the older and conflicting option uaegfx_card = 1.
So in short, just remove
from your configuration file, and then try!