OK, inserting the "not needed" Layers 2 to 15 into a 2 Layer Layout manually by edditing the *.brd file is strange - BUT ! works !
Maybe the AutoDesk coders can have a deaper look into this issue.
I found in my *.brd file:
<layer number="1" name="Top" color="4" fill="1" visible="no" active="yes"/>
<layer number="2" name="Route2" color="16" fill="1" visible="no" active="no"/>
<layer number="15" name="Route15" color="23" fill="1" visible="no" active="no"/>
<layer number="16" name="Bottom" color="1" fill="1" visible="yes" active="yes"/>
Yes, I have the "Standard" License with up to 4 layers, so that makes sense - somehow, but I have no Layer 3.
So why the error "Layer 3 missing"" or in my case "Unbekannter Layer: 3".
Also in the eagle.scr I found all 16 layers activated for "Preset_Standard".
But even deleting Layers 2 to 15 in the eagle.scr file does not solve this issue.
So, THANKS for the "edit the *.brd file" workaround, very much.