I suppose it is the following problem:
You must do things in the following order:
1. Enable permalinks (write access to .htaccess required)
If your .htaccess file were writable, we could do this automatically, but it isn’t so these are the mod_rewrite rules you should have in your .htaccess file. Click in the field and press CTRL + a to select all.
2. Hide backend (permalinks required)
3. Remove write access to core files (.htaccess et. al.) if really wanted
Due the fact that Better WP Security is not able to reset the write access from disabled to enabled, this order is required