Without looking deeper into this, I would highly suspect that window manager hints (such as those specified in
ICCCM and
EWMH) are not applied completely correctly. But you should first ensure that GNUstep is indeed doing something wrong; it is also fairly possible that OpenBox doesn't do things correctly. What happens with Metacity and WindowMaker?
I'd start investigation by trying to use
wmctrl to determine EWMHints -- I never used it, but it claims to be able to interact with EWMH atoms -- and xwininfo to determine ICCCM-defined things. Then I'd try figuring out where the incorrect stuff is done in gnustep-back (if it's done incorrectly at all).
While cursorily reminding myself of the specs, I ran into the suggestion that EWMH window type stored in _NET_WM_WINDOW_TYPE should determine the window order, as should _NET_WM_STATE_ABOVE.
So I'd start investigation by looking at interaction between OpenBox and value of _NET_WM_STATE/_NET_WM_WINDOW_TYPE.