I had the same issues mate on Vista
(
You have to install the game in Administrator mode, this then sets the editor as Administrator privledges, then right click the Editor.exe and set to "Run as Administrator". If you dont, your maps and resources are deemed as unknown items and they are placed in a quarantined "Compatibility" directory.
To find you files, go to the Men of War directory, navigate to your mods folder, there should be a "new" option on the task bar at the top of the window, which says "Compatibility Files", select this and your files will appear, but not in the current directory, but in a seperate directory accessed via your my documents folders
You will have to either do this everytime you use the editor or copy the files from there, into your mods folder and then set the editor to "Run as Administrator".
I found it easier to just re-install the whole game, but first, run the setup.exe as Administrator and this problem disappears.
Bloody Vista and UAC are too clever by half!!