One of the changes in recent revisions 9059 or 9060 makes the pencil tool act strangely with default snapping settings (global node snapping enabled) while a grid is visible and set as active snapping target: it seems as if some key press or release events don't get processed immediately.
To reproduce: draw freehand curves with different mouse speed and timing of left-mouse-button-clicks. Sometimes neither the path outline while dragging nor the finished line when releasing the left mouse button are visible, yet the starting point is picked up for and added to a later drawn curve.
It does not happen with no grid visible nor when global snapping is disabled. This is reproducible with my usual preference settings as well as with a default (new) preferences.xml file.
I haven't seen it in earlier revisions <= 9058, but can reproduce it with Inkscape 0.47+devel r9060 and r9061 on OS X 10.5.8
~suv