I've experienced the same thing on an X60s.

When I suspend and resume while attached to the "ultra base" docking
station the middle mouse button returns to default behavior (paste), and
if reissue the xinput commands it makes it so middle click no longer
pastes if held down for a while (presumably for "Wheel Emulation
Timeout"), like when wheel emulation scrolling works, except no
scrolling happens.

When I suspend and resume while not attached to the docking station,
middle mouse button is reset to default behavior, but reissuing the
xinput commands does make scrolling work again in this case.

-- 
Wheel emulation doesn't work after suspend/resume
https://bugs.launchpad.net/bugs/289023
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