I don't know if it's related to fluxbox, but whenever I launch the transparency management at startup with
xcompmgr -f it becomes difficult to use pop-up windows. They are all sent to background, and the main application windows remains on the top.
It's pretty unusable with applications that have much use of pop-up windows. If I don't launch xcompmgr, the window behaviour is ok.
Any idea what to check, or to do ?