Ok, after more searches and poking around I believe I have discovered
what is wiping out the xmodmap. I went into "Regional & Language ==>
Keyboard Layout" and then select the "Xkb Options" tab. I noticed a
checkbox on that tab: "Enable xkb options". The checkbox was checked,
but down below in the Xkb Options there were a whole slew of options to
select but not a one of them was selected. So I unchecked the "Enable
xkb options", logged out, logged back in, and voila! Now my xmodmap
settings are back. I am fairly certain that I never went in and turned
on the "Enable xkb options" box. This is especially annoying since no
options were checked.

Since it seems that running setxkbmap will wipe out any xmodmap settings
perhaps This should be run earlier, like in an earlier entry in
Xsession.d?

-- 
xmodmap fails in Xsession.d
https://bugs.launchpad.net/bugs/251247
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