With some detours, I finally got the elevation profile working in my mapset ;-)
I dont know if it now worked because I also installed Garmin Basecamp.

First, I had all map tiles and contour img's in one mapset.
They are still there, but now I created another tdb index file
with mkgmap on all contour img's from the same mapset, with the options:
--overview-mapname: contours_nl
--show-profiles=1
--tdbfile

I stored the contours_nl.tdb file and contours_nl.img overview map in the same 
directory,
and installed it in Mapsource. 

The result is that I see the contours on top of the map (with routing), and I 
can choose to switch
to the bare contour mapset without all osm data. In this mapset I can see now 
the elevation profile :-)

On the GPS (tested a Etrex and Dakota) I can now switch the contours on and 
off, 
but routing doesn't show the elevation profile.

You can download and view some images of my custom maps on my website: 
http://sites.google.com/site/openfietsmap

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