The problem is quite simple. (In cases like this I find
WinMerge invaluable as I can simply examine both the .FS2 and .BAK files and see what changed).
What's happening is that FRED is copying all the comments to the new file. But since it did manage to parse the comments into real ships it's trying to write the real ships into the mission file too. After saving a mission FRED immediately reloads the mission it has just saved. Only problem is that now it has two ships with the same name. Hardly surprising it's crashing then.
Not sure what you can do to solve the problem to be honest.