My guess is during the renaming process. Make sure each file retains its original file-type, so NewMap.mis, NewMap.ter, NewMap_sg.ml, NewMap.ml. But I already found a quicker way of doing this and posted about it in the Map Editor thread.
When you open a map you want to edit, go to File > Save Mission As, and type in NewMap.mis in the Save As box (it doesn't have to be NewMap, just name it whatever you want). You
must include .mis at the end or else it won't work. This will create NewMap.mis and NewMap.ter files. You don't have to mess with renaming anything.
Add NewMap to the server config file like you normally do, host it, and relight it. This will create the lighting file (.ml). That should be it. I have created a video on how to do it below: