I'm sorry Fluxbox....

Like I said, I'm sorry Fluxbox for doubting you, you do still work well. I've enabled xcompmgr - which is an 'X composition manager' or 'xcompmgr is the standard composition manager for the X Composite extension, which allows clients to modify what is drawn to the screen before it happens. This composition manager implements shadows, fading, proper translucency, and more.' I've put it in the startup.sh so its called when I log into fluxbox, and this seems to have got rid of my two show-stoppers. Cairo-dock is now at the bottom of the screen, in its proper place, and urxvt is now not hiding under the panel. So its business as usual again!