I have concluded that combinations in prestashop is BROKEN. I found a workaround but it is completely stupid that it works like this.
1.Firstly create all your combinations but do not give them any prices.
2.Go to Prices and scroll down to specific prices select the combination you want,
3.uncheck "leave base price"
4. place your price in Product price (tax excl.)
This is completely stupid and by no means should it be done like this. I have NO idea how or why this works but combinations doesn't
Let me know if this worked for you.