thanks for the plug kitkun.
it sounds like you need to edit the galaxy.manifest in the entrenchment folder
add the extra maps names to the bottom of the file and alter the maps count at the top.
the map converter only updates the map format from earlier to 3 with the changes for normalstart & quickstart.
also there is a rumour that the galaxy.manifest might vanish in a future patch, which would eliminate this type of problem.
hope this helps