Could you let us know a bit more on how the problem occurred? Were you running an earlier version of Fedora and then updated to 39 and then the AIJ interface coloring changed, or is this your first use of AIJ under Fedora? Or, did a previous version of AIJ work fine with Fedora 39, and then an AIJ update broke the interface coloring?
Actually, another question: Which type display adapter are you using? If you are using AMD, I have seen reports for other Fedora 39 display problems that setting "amdgpu.sg_display=0" fixes the display issues. I'm not a linux user, so I'm not sure exactly where to do that, but try that approach and let us know if it resolves the issue.
If you roll back AIJ to version 5.2.0 or 5.1.0, does the display problem go away (when running Fedora 39)? You can use the update facility at AIJ_Toolbar > Help > Update AstroImageJ to do the roll backs, and then return to the daily build when you are ready.
I see this note on an ImageJ post "Fedora 39 using “GNOME on Xorg” shows the correct toolbar." I'm not a routine linux user. Are you using something different than “GNOME on Xorg”? If so, is it possible for you to try this combination to see if it fixes AstroImageJ also?
Thank you very much for your reply. I do use a Wayland environment on F39. The change from Wayland to Xorg may resolve this problem. But I used a Wayland environment in F38 and the AIJ icons had the right colors.