From the 4.11m readme:
Mouse wheel zoom
It is possible to zoom in/out with the mouse wheel on all maps (Briefing, Debriefing, FMB and inflight map). The new view is centered on current mouse cursor position if possible (exceptions are near the map edge). If you use mouse wheel as one of your HOTAS commands the zoom in/out feature is disabled on the inflight map.
So check to make sure mouse wheel isn't assigned to something else.
If It is, obviously, kneepad (or full screen map) zoom via the scroll wheel won't work.