I assume you're using the official map editor. This might be a long shot, but try downloading this one and replacing your current map editor .exe with it
viking .. gurut .. org / Map_Editors / Supcom%20Map%20Editor.exe
Replace double dots with single dots (sorry, the forum is preventing me from posting URL's so I gotta do this weird way).
... i suggest this because one time I did a reinstall of supreme commander and pulled an old copy of the map editor I had on my com and installed it. then the editor kept crashing every time i opened a map or even started a new map.
then I downloaded the one from the link above, and noticed that the file size was actually different from the old map editor I had (difference of a few bytes only) even though the file name was exactly the same "Supcom Map Editor.exe" ..... so perhaps there were different versions of the map editor -- all having the exact same file name and so almost impossible to distinguish between them. one of them keeps crashing (on some coms), and the other doesn't. so try that one and see if it works.
-Mark