The coastlines are rendered from shapefiles, try to look at your shapefile in other tools first and compare in what way they are different. I can confirm that mapnik can render shapefiles fine, since I’ve created my own, I had no problems so it would be interesting to know what you problem was.

GPX->osm: Try to make a simple import first then go back and see what you did wrong.

This should work, it’s just reality messing with the results again.