Hi!
I'm so sorry for the delay in replying you. I was on holidays for the last few days. I ran into this issue while preparing a map with a few hundred POIs to take.
You are right, of course!
At the last minute, I found that the issue was in the installation procedure.
I was running MapSource 6.13 in my old EeeePC (Windows XP), and I was using MapSetToolkit to install the maps via freeware cgpsmapper.
Somehow, the end result was having the maps installed as being NT, and Mapsource refusing to install them into my Garmin Quest.
I solved this by updating Mapsource to a newer version (6.16) and using JaVaWa GMTK to install them.
I still had to pack and catch a plane, so I did not post that info at the time.
I'm not sure why the issue arised, but it ain't an issue of mkgmap for sure. :)
Thank you for your reply!
Nuno Pedrosa.