Hi, jazzbiker. Thanks for the input. Correct, $HOME is not in .filetool.lst, just selected subdirectories of $HOME.
Actually, I've refined my understanding of the problem: ~/.X.d/startup-scripts is there, and most of the jobs it lists get run. The one that tends to fail is xbindkeys & which is important to me because it enables all of my keyboard shortcuts.
I'm going to assume that xbindkeys sometimes butts heads with something else at boot. Will adding sleep 1 before it and see if it helps.