If you use the Standard Scalos AROS 68k version, you will have the same problerms as AROS x86, see screenshot.
With Def_Icon AROS native, you get the right icons and tool assigned, but if you use other Icons like Glow Icon, Power Icon or Icon PNG, they will be ignored and therefore not displayed.
On your system you probably mixed OS3 files and settings, so all tests will not match those done with just the AROS tools