is the app that makes the window called emacs-a and emacs-b? fluxbox doesn't need to remember the window position of scripts unless they actually open a window. I suspect what is opening is two instances of emacs (name=emacs, class= Emacs), with different configurations. so in effect, your name=critera is not being met in the app file.
what you need to do is make 2 symlinks, unique, to emacs. then launch emacs with the symlinks. fluxbox will treat the symlink names as different.
here's a simple example apps file using leafpad. in the example, leafpad2 is simply a symlink back to leafpad.
Code:
[app] (name=leafpad) (class=Leafpad)
[Workspace] {0}
[Jump] {yes}
[Close] {yes}
[end]
[app] (name=leafpad2) (class=Leafpad2)
[Workspace] {1}
[Jump] {yes}
[Close] {yes}
[end]
the first starts opens on workspace 0 (alpha). the second to workspace 1 (beta). I set mine to jump to the workspace when opened but it isn't necessary.