> I looked at the code and cannot see how this could be happening.  The
> region face is set to ns_selection_color in ns-win.el, but this
> should be overridden by .emacs read later.

It probably should, but it doesn't seem to.

This bug is easily fixed by changing the following line in ns-win.el:

(set-face-background 'region "ns_selection_color")

To:

(if (not (face-attribute 'region :background))
    (set-face-background 'region "ns_selection_color"))

Tested and confirmed on a git checkout from 8/14.

The real fix may be to change when ns-win.el runs, but I didn't look into that.

Thanks,

Luke