To solve your problem, there are always cheat codes

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For what it's worth, I've encountered the same problem (making tweaks here and there). Some missions I was able to fix by manually making all ;; FSO 3.9* background stuff default and deleting the retail compatible parts, and a few still refuse to work. I can open and edit fine (even sm1-01a, as above), but I get that string of errors after saving, and it ruins the file. Opening the file in a text editor, it appears FRED stuck a chunk of mission in the wrong spot, and it can't be opened by FRED. His log looks like mine: background info stuffed into earlier sections of the mission file throwing errors.