I'd be curious as to what, specifically. I think the best way to get help here would be to say something like, on Linux, I can do X, but on FreeBSD that configuration option is missing. Hopefully, someone will see that and be able to help. Or even something like on Linux, Fluxbox consumes X amount of resources, but on FreeBSD, it is consuming much more, with specifics, such as processor time, memory, whatever. It may be that the Fluxbox developers use Linux, and have made some adaptations that work better on Linux.
So, if you could give a few specifics, it's possible someone may have answers.