The Edge Boundary Checking mode isn't meant to "slice" the geometry, it's removing elements within one item that are "based out of area used for distribution". There is no "physical cut" performed as this might be extremely resource demanding on large distributions and this "trimmed part" is treated by the render engine as a kind of "Matte object" internally. This way it doesn't affect the overall performance as massive geometry slicing might require huge additional resources.
In this case you'll archive better results using a very simple style in the RailClone plug-in, which will slice the source geometry and handle these "problematic" areas easily. Hope that helps.