Need Help with FF3 Level Editor

They should and do work together. I use both programs synonymously. My guess is that sadly, you will need a new fresh ROM. Somehow the data in the ROM has been corrupted and the Map Editor can no longer read it. To see what I mean just try to edit the "Big Quotes" with a brand new ROM, save, and then open the ROM up in the map editor. It should work! If it still does not, and you still get that error message, then that makes no sense and we will continue trying to solve it. Have you applied any patches to this ROM by any chance? I used to get a bad error message like that with my totally hacked messed up ROM. Not quite to that extent of shutting itself down though 0_0