zetox : I think u r facing this problem because the program being used to set the background doesn't support transparency...use something like Esetroot which does.
The command for setting the background would probably be in the 'style' file for the theme u r using. I am using the DEPTHCORE theme which has a line like this in it :
rootCommand: Esetroot -stretch ~/.fluxbox/backgrounds/depthcorekernel.jpg
darrel.com : Unfortunately for us , I dont think X supports TRUE transparency, like what u described.... I think what all these so called 'transparent' apps...just take a shot of the underlying wallpaper use that as their background or somethin....
zetox, I suggest u switch to something like aterm or eterm , they aren't as resource intensive as gnome-terminal and support transparency and tinting and stuff...
hope this helps,