[GraphHopper] Strange results for GraphHopper paths

[Joel Haasnoot]

Hi,
I've been using the ngmip fork of graphhopper for a bit of an
unconventional use - to route railway segments (many would call this
"one big hack").

I've got a shapefile of all the railway lines, that's been converted
into an OSM file with JOSM, marking ways as 'highways="primary"'. I
then route between each unique pair of train stations in the
Netherlands by coordinates, to be able to create national map based on
precomputed segments, to be able to use for disruptions and individual
trains. The reason I'm using the ngmip fork is to be able to route
between these arbitrary coordinates - stations are often halfway
ways/noes.

So far so good, but as of yesterday, making any change to the OSM file
in JOSM is creating very strange paths. Even the smallest change in
totally unrelated ways is triggering "flipflopping" - see this
screenshot: http://i.imgur.com/hqpozAi.png
I tried doing a diff between the two OSM files, but it seems more than
just deleting a few nodes is happening.

Does anyone have a sense of what might be happening? Is this a JOSM
bug, or is it related to how GraphHopper handles OSM? Or is this an
issue specific to the ngmip fork?

If need be, I can upload the correct and misbehaving OSM files.

Thanks in advance,

Joel Haasnoot