Johan
I think I am just stupid.

You know what, you have pointed me in the right direction. The whole afternoon I was fiddling around with Basecamp and Mapsource. Reading Help files and what ever stuff. In the end It was my own stupidity. I never actually made waypoints and connect them afterwards to form a route. I only made a route with via points. So if the gps find there is a better way between two via points, it will take that way. That is why I was thinking all along that Mapsource is throwing away my waypoints. I did not make any.
So I made my waypoints, connect them to make a route and wallah, Mapsource allow me to send them to the device as you told me to
And is actually very easy to do.
Thanks again.
Regards
Martin