i found this in #fluxbox/freenode, when typing ",xorg" the bot will tell you... There are some weird problems with Composite enabled on new X.org. To workaround them, set the slit layer to "Desktop" (flux menu -> Configure -> Slit -> Layer -> Desktop), OR apply this patch: http://www.cse.unsw.edu.au/~simonb/fluxbox/fluxbox.xorg_composite_fix.patch so maybe put the patch in the tree?
Uh, yeah, wait for -r3, it'll have a slightly better version of that along with a few other fixes.
included in 0.9.10-r3