This is just a very weird problem.  It's almost definitely Unity
related, since if I run classic desktop, my xmodmap will always work.
Frankly I suspect a race condition because sometimes after first login
with Unity, my xmodmap will work, and other times it won't -- but only
partially.  Here's some of what I've seen:

Log in with Unity, apply the xmodmap.  Alt gets mapped to Apple/cmd for
things like the switcher, and Super calls up the Unity search, but
Alt-<key> doesn't bring up the menu bar in Terminal, or get mapped to
meta in Emacs.

Log in with Unity, run gpointing-device-settings to fix the cursor, then
run xmodmap.  Now it everything works fine.  (I suspect it isn't the
actual running of g-d-s but the time between login and xmodmap).
However, this isn't completely reproducible, because sometimes you get
the above behavior.

Note that once the xmodmap is only partially applied, nothing seems to
be able to make it fully applied.  Also, xev is completely unhelpful
because no keypress event is registered.

I think what's happening is that Unity is capturing certain keypresses
before xev or the applications see it.  There's a timing issue also so
maybe when Unity is not quite done doing whatever magical thing it does
before xmodmap gets run, it just hoses things permanently.  I *think* a
re-login won't fix this and you need to reboot, but I'm not positive
about that either.

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https://bugs.launchpad.net/bugs/771246

Title:
  remapping alt key loses keyboard shortcuts

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