Since this problem is not yet addressed I decided to post a new thread about it. Hopefully the Devs will read it.
Everything was working mostly fine until I decided to test publishing of a Mod on Steam. Next time when I started The Divinity Engine, the Story Editor started to throw the same old "Read Only Error" on my face again when ever I try to modify something. Actually I have never been able to create a script in a story editor because of this error. Instead I have created empty file template manually first, so that I can start editing it in the Story Editor afterwards.