Polygon Intersection with Line | Python Shapely

Shapely is built on top of a C wrapper around the C++ GEOS library. Somewhere deep inside this C++ library sit the Precision classes which handle roundoff errors. I think we may conclude that your version of Shapely, and the geos libraries, handle this case differently. Unfortunately the code that accesses the precision model is not available in the C api, and therefore neither in Shapely. See http://lists.gispython.org/pipermail/community/2011-February/002898.html

Changing to a higher version of geos might solve your issue, though. It works fine on my machine with shapely 1.2.16 and libgeos 3.3.5-CAPI-1.7.5.