Here's the relevant excerpt from
https://bugs.launchpad.net/ubuntu/+source/eclipse/+bug/779416 (#42 just
gives the fix but left out source of fix and description of what was
tested):

----

Removing this environment variable from the startup script
/usr/bin/eclipse fixes this - the thumb is drawn and usable.

 export GDK_NATIVE_WINDOWS=true

Where possible I tested the problems listed in #443004 (and it's dupes)
and they no longer seem to occur - I presume that the bug in GTK which
provoked this workaround has been fixed.

Suggest removal of the workaround from the startup script

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https://bugs.launchpad.net/bugs/769277

Title:
  Eclipse shows overlay scrollbar but when i hover there is no scroll
  handles

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