It sounds like you're bringing up two separate issues here. The first is Fluxbox transparency. Given that CentOS/Red Hat are not bleeding edge distributions, you may be using a very old version of Fluxbox. The development version of Fluxbox is easy to install, and I've never had problems building it, even on distros with older libraries.
edit: The easiest way to get the devel version is to use their git repository. If you have the git tools, you can get the code thusly:
Code:
git clone git://git.fluxbox.org/fluxbox.git fluxbox.git
Run:
To prepare, and then build as normal./edit
Fluxbox does not manage transparency for applications themselves, only for window decorations. So, getting transparency with aterm, eterm, rxvt-unicode, or any other term emulator which suppports it, is a separate issue. These applications can be run with an argument that sets the transparency level, or can be controlled in each user's ~/.Xdefaults file.