Resolve "wrong start and end of reaction lines"
This MR should resolve the problem. The root cause was ignoring layout of reaction with single line segment (in reaction part) when there were more than one product or more than one reactant.
However I found inconsistency in your SBML layout file. According to SBML specification(http://tinyurl.com/sbml-layout-rc2):
“product”, “sideproduct”, “substrate”, “sidesubstrate”, “undefined”: The line segments have their start element at the ReactionGlyph and their end element at the SpeciesGlyph.
But the point order in the submitted SBML file is reversed.