Hi,

see first
http://gis.19327.n5.nabble.com/merge-lines-and-routing-tp5758913p5759595.html

I think the reason is the remove-short-arcs processing. This can move a road,
esp. if you use a rather large value like --remove-short-arcs=5.4. In the example case, way http://www.openstreetmap.org/browse/way/27904971
is moved towards
http://www.openstreetmap.org/browse/way/217767494

Now, the overlaid line with  type 0x10650 (really this invalid extended type?)
is not a road and stays where it belongs. Another possible effect would be that the road
is deleted while the copy is not.
I think the solution is to make sure that
1) all lines created from the same OSM way have the same points after
short-arc-removal was done with roads only
2) if short-arc-removal deletes a road (e.g. because it only has one short arc),the other lines
for the same OSM way are deleted as well.

Attached is a patch that implements this, a compiled binary is here:
http://files.mkgmap.org.uk/download/120/mkgmap.jar

Gerd