You've just hit upon something I've been struggling with lately too. It seems that when you build fluxbox or blackbox from source, the installer does not quite take care of everything it ought to in order to make those available from your graphical login screen.
Anyway, what I had to do in order to make mine work was this: Look in the directory:
In there are several small scripts called GNOME, KDE, etc. Create a new script for fluxbox, simply called fluxbox. Make it similar to the others, something like:
exec /etc/X11/xdm/Xsession fluxbox
(or even just "exec fluxbox" might work). Anyway, make sure it's executable (chmod +x fluxbox). You will probably also need to create a file in /etc/X11/wmsession.d. In there are files called 01KDE, 02GNOME and stuff like that. Create a new one with the next avaiable number, like 03FLUXBOX. Copy its contents from one of the existing ones, and tailor it to run fluxbox instead. This file doesn't need to be executable.
As for getting the .xsession file to be read from yor home directory, I had similar problems with that. I wanted gkrellm to start up when I ran blackbox, so I added stuff to that file; however, due to the complex series of scripts that causes my window manager to get loaded, the .xsession file was ultimately ignored. In order to make X read that before starting up, create a script called, for example, /usr/local/bin/startfluxbox. Make it look like this:
if [-x $HOME/.xsession ]; then
Basically all that does is say "Does this user have a .xsession file? If so, run the commands found in it, then load fluxbox." Anyhow, once you have that (make it executable too), modify the /etc/X11/gdm/fluxbox script above to run "startfluxbox" instead of "fluxbox".
I hope all that made sense! Good luck.