Minimal install, apt fluxbox issue
 

[Edit]
Solved, just needed to run "update-menus"
APT wasn't auto updating the menus when using it to install new applications (Something that is working fine automatically on my AMD64 install now though). Running "update-menus" automatically updates them. Though it will overwrite the menu file with a new one, erasing any custom changes you have made.

restart the xserver log out log in