Configure Hero
 

When ever I start the program or make a new hero there is always three books unchecked from the settings. I have to manually select them every time. I have tried adding them and set the settings as default, but next hero has those same three books unchecked.

Is there a way to keep those three books checked? They are under the User Content section.

If you set what you want as Default, then any new portfolio you create will have those settings.
Any portfolio that you had previously created will not - you would have to go through EACH hero and click on "use default". If you load a creature using the encounter builder, it will not have your defaults either.
It would really be nice to have a button that changed all heroes in a portfolio to default at once.

I have set them as default and each new character I have to choose those three sources again.

When you say "each new character" are you creating them in a new portfolio, or an old one?
If that's a new portfolio, then something is happening that I don't understand. Maybe send an email to support and they might be able to work out what is happening.

Yes each new hero either by itself or within a portfolio.