The resources are stored in the X server - this is to prevent need for distributing the configuration files across several computers. .Xresources was never meant to be read by the applications, it is loaded into the X server with xrdb (although the situation is slightly more unclear when it comes to the older .Xdefaults, AFAICT). See wikipedia article for explanation.

That said, your remote XTerm tries to get its resources from your local X server, probably doesn't find them and resorts to defaults (which is black text on white background). Either load the desired settings with xrdb -merge into your Xserver or use XTerm options to achieve the desired effect: xterm -bg black -fg grey

As a side note: if you are running xterm remotely, chances are that a terminal multiplexer (e.g. tmux or screen) running on the remote machine might do you a better service.

Running an xterm remotely with ssh -Y, defies the coloring I setup in .Xresources
Is it possible to use the Apple remote to control Keynote presentations? How so? I have a mid-2010 white plastic unibody MacBook. (I've been told that this isn't supported, but perhaps there are third party solutions.)
