After a bunch more digging, it is in fact an issue with xmonad's focus
problems. I added the following to my xmonad.hs to deal with it:
myManageHook = composeAll . concat $
[
...
[ resource =? "xfce4-notifyd" --> doIgnore <+> doF W.focusDown ]
...
]
The notifications still popup over the xflock4 window which means that
people can read my messages, but that is very minor, and only occurs on
my work computer despite my home computer having the same set up.
This ticket can probably be closed. Sorry for the trouble.
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https://bugs.launchpad.net/bugs/1020948
Title:
xfce4-notifyd steals window focus, even from xflock4
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