Fluxbox 0.9.14-gentoo-r1 aterm version 1.00.00 Fluxbox will not allow applications (specifically aterm) to set their own *borderWidth & *borderColor. The resouces borderWidth & borderColor usually set in the styles config however do work. If I comment those out from my style and load Aterm*borderWidth and Aterm*borderColor they just don't work. Also tested with aterm-0.4.2-r11. Have yet to try fluxbox-0.9.15.
Same issue with fluxbox-0.9.15
This is not a bug. From the ICCCM (http://tronche.com/gui/x/icccm/sec-4.html#s-4.1.5): Clients should be aware that their borders may not be visible. Window managers are free to use reparenting techniques to decorate client's top-level windows with borders containing titles, controls, and other details to maintain a consistent look-and-feel. If they do, they are likely to override the client's attempts to set the border width and set it to zero.