I don't think these warnings are bogus. Mkgmap definitely has problems with multipolygons. The Languedoc-Roussillon extract (southern France) from Geofabrik provokes about a hundred of these warnings. But I believe that the intersected ways are being generated by mkgmap and that the OSM data is OK. Mkgmap-r1475 did not have this problem but r1502 and r1507 both do. I am unable to pinpoint more accurately when the behaviour changed because I do not have copies of the relevant releases. Perhaps r1494 could be put back on the web site, in the hope that we might have the benefit of the fixes to generate-sea without the multipolygon problems. Exactly where the problems show up can depend on where the tiles are split. One example is at http://www.openstreetmap.org/?lat=43.4047&lon=3.5107&zoom=13&layers= B000FTF as seen on Lambertus' site. Take a look at his tile 63240406.img dated 20-01-2010. If you look at the vineyards (land-use polygons) in the vicinity of Pinet, you will see an obvious straight edge which is spurious, and areas where the inside and outside of the polygon have swapped over.