all that it does is cause tint2 to switch to the top left and windows borders disappear
Those are the only issues? You can otherwise use fluxbox as intended?
Thought about this some more, the closest I've come to an issue like this is when using tmux or emacs with fluxbox. Starting either, wouldn't crash the window manager, but fluxbox wouldn't respond correctly to any mouse or keyboard input - like it got reconfigured.
Turned out to be a key binding collision between fluxbox and either tmux or emacs. Made a couple changes to ~/.fluxbox/keys and tmux.conf and all was right with the world. Does nomachine have some default keybindings so you can administer the system from a console? If so, see if they conflict with your ~/.fluxbox/keys file.