No, has nothing to do with Windows versions, or at least it shouldn't have. Check resources.cfg for the paths. You could try a quick thing: copy the missions folder from Data/missions into root directory (so you'll have Dune2000/missions) and see if it makes a difference. For example, I have my missions folder in the root directory, not in Data.
I tried to change the paths to look similar to yours, but now when i try to test it says "Invalid filename".
My version is also 184.108.40.206 , i even installed everything on 2 seperate laptops to see if the results are different and it turns out its the same thing.
The maps (original and new ones) are in the Gruntmods studios/Dune2000/data/Missions folder, i am not sure where the editor is looking, but when i copy the TESTMAP.mis file to Dune2000 folder, it looks in the Gruntmods studios/Dune2000 and launches an unsaved map and only that one, selecting other maps to launch it will launch mine again, also my actual map has more objects while it loads up the one i saved quite some time ago.
I didnt try to edit the resources.cfg yet...
from what i've heard, maybe its because i have windows 10?