X and Fluxbox :: Startup applications....
If you set the background with a script prior to running Fluxbox, the background will change again through either the style or .fluxbox init.
If you add the script after the fluxbox line it won't run until after fluxbox closes, which is pointless (unless you want to manually restart fluxbox every time you log in).
What you could do to make the background script run automatically and stay is to use it as the rootcommand in either .fluxbox/init or in your style file. Using it in a style will run the script only for that particular style. Using it in init will override all style root commands. Reloading fluxbox in either case should rerun the script and you'll get a new background (just guessing...haven't tested it).
rootCommand: /path/to/script
or
session.screen<number>.rootCommand: /path/to/script
Ok borrowed a style, made a copy and appended the line. Works fine now! cheers! 
original here.