While experimenting with motorway-junctions and links, I noticed that MapSource draws some kind of "ghost" route on my minimalistic map (see attachment). Does this indicate some kind of mkgmap problem or is it simply a bug in MapSource?

In earlier times I've seen such disappearing lines one my gps unit too, so I assume it is not mapsource having a problem, but some errors in the img file. Are you using the latest revision of mkgmap?