Problem with theme editor

I couldn’t find any info on this, so I’m posting here in hopes that someone can help me out.
For some reason my theme editor stopped working. I’m using version 2.0.
When I click on a file I want to edit, e.g. the header, it only forwards me to the main blog page where my entries are. Same goes for trying to switch between the themes.
The only thing I can think of that I changed was, that I changed my permalinks from %postname% to index.php/%postname% since it gave me troubles with newly created pages.
But I use the same format on another blog and don’t have this problem there.

Thanks for any help. 🙂