I am having the same issue, with gedit and evince not scrolling with mouse wheel, except it is when the keyboard focus in on another window (e.g. terminal) but mouse focus is on the first window (I am not sure what precisely is meant by mouse being hidden, so I cannot confirm this aspect). I do not have this issue with gnome-terminal or chromium.
I have just upgraded from 12.10 to 13.10 (via 13.04) and this is when the issue started occurring.
I am having the same issue, with gedit and evince not scrolling with mouse wheel, except it is when the keyboard focus in on another window (e.g. terminal) but mouse focus is on the first window (I am not sure what precisely is meant by mouse being hidden, so I cannot confirm this aspect). I do not have this issue with gnome-terminal or chromium.
I have just upgraded from 12.10 to 13.10 (via 13.04) and this is when the issue started occurring.