Go to the "Character" menu, and select "Configure Hero".
Make sure your three allowed books are checked: "Advanced Class Guide", "Advanced Player's Guide" and "Advanced Race Guide". The core rules are included by default, so you don't need to check anything for that.
Scroll up and down until you get to "Advancement Speed", and make sure everything else up to that point is unchecked.
That should give you your allowed rule set and remove anything else that might be interfering or changing things.
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