I see the same issue after upgrading (yes, just recently, I'm a slacker)
to 13.10 from 13.04, on evince and nautilus.  I too am running XFCE.
(Specifically 4.10)

Hovering over those applications and using the scroll wheel still raises
them, just as if I'd clicked on them, but does not scroll them.

"click scrolling" (as described above by Willy) does cause the
applications in question to scroll.  The click functionality of my
scrollwheel is normal unix middle button behaviour.

I will try the PPA listed above and report back.

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https://bugs.launchpad.net/bugs/1171342

Title:
  mouse scroll wheel not working in gedit & System Monitor

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