I finally found out what's happening - the default color for the background has changed. If you run 'xrdb -query | grep Back' you'll see that the background color has been changed to #fffff0. If this resource is removed, the problem with viewing the 3D effects of the buttons in Xemacs and other programs, e.g. tkhylafax and exmh, goes away.
I can't figure out where in the system that this resource is being set, so I've put a script in /etc/X11/xinit.d that has the single line: xrdb -remove "*Background" Now the background color for Xemacs is it's old, nicely contrasting gray, and xterm's come up with a white background instead of dirty yellow.
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