This seems related to an open bug:
https://bugs.eclipse.org/bugs/show_bug.cgi?id=110916
I had this problem for 1 whole day, made several restarts, clean registry, memory was ok, mouse and touchpad both had this behaviour with cursor keys and menu selection or component window focus change.
Then I came to work after shutdown 2 days afterwards and all is ok.
Bummer, but better no bug than a bad bug.
Cheers,
JN