@Siem, I've modeled your settings in a local test site, setting Alternate URLs end with to blank like you have. With that setting, the default .htaccess file and enabling the language sidebox, I get a link that looks like http://localhost/testsite/index?language=en which properly displays, when clicked, the main page.

Perhaps there's a setting in your .htaccess that's a bit off; if you'd post its contents wrapped by the CODE tags (the big # above the post-writing textbox), perhaps that would provide a clue.