It’s been awhile since I’ve used Mappy, but I recall a problem where switching between tilesets when you have a map open causes the program to get confused for whatever reason which tiles are which when it comes time to export it as a .MAR file.
BwdYeti’s FE Map Creator allows you to import a map by selecting a tileset and then giving it an image of the completed map, which it then turns into a proper map file by matching the image with tiles on the tileset. I’d feed it a screenshot of your map from Mappy and re-export it as a .MAR with the Map Creator tool, that should hopefully fix it.
If it’s a vanilla FE6 map you’re using, the tool already has all the maps from vanilla FE6~8 included in the download ready to be exported as .MAR files.