Hi,
 
I've load from OSM rectangle
bbox=24.061,35.2895,24.2976,35.4638
using Overpass API export.
 
(this is part of Greece > Crete)
 
There are among other things 2 polygons nature_reserve (140514809 and 140515050) and polygon natural water (356673828).
 
I use the newest mkgmap 3909 (Windows 10).
 
After using mkgmap with option file:
 
family-name=fam-name-kreta
gmapsupp
output-dir=D:\Dokumenty\OSM\ttt\
description=descr-kreta
unicode
index
route
precomp-sea=C:\Users\Darek\Downloads\sea.zip
generate-sea
order-by-decreasing-area
mapname: 63240001
input-file: map.osm
 
 
After generating gmapsupp.img and transferring to Orgeon 650 unfortunately I don't see neither polygons (140514809 and 140515050) nor polygon (356673828). 
 
 
What I do wrong? 
 
Best Regards
Dariusz Kwapisz