Maybe your conf file contains old-and-not-anymore-used settings? I 'm asking because I get nowhere near this size for .conf files...
It's due to the Squirrel lexer. The keywords section ends with a backslash and a newline. Remove the backslash, and it works.
I don't know why, but EditorManager fucks it up because of that. Maybe it is a bug in tinyxml's CDATA handling too, no idea.
What happens is that each time the config is saved, another newline is appended to the CDATA holding the Squirrel lexer.
Apart from this obvious bug, it once again opens the old question why we must save every single lexer to the config file. They do not belong there...