First you should update to 3.5.6. This can easily be done with extension easyupdate3. Then you should try in safe mode which disables all extensions. Then you also can try the option "enable auto_item".
What is the reason for wanting index.php in your URL? Without it URLs look more friendly and readable.
Code:
example.org/index.php/my-page.html
example.org/my-page.html
Don't forget to rename your .htaccess.default to .htaccess.
If in the end you can say that it's a bug (tried with a clean installation) you can open a ticket at github.
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