Hello,
The fact the the product is added to the cart with the wholesale price is correct.
Indeed I don't see any restriction on the quantity or usergroup so the lowest price is used in the cart.
Be sure to add price restrictions if you put multiple price through your product configuration page.
Where exactly do I find the option in your configuration to change the display from the lowest price instead of the highest one in the shopping cart?
Xavier was talking about the "Price display method" option of your product listing content menu / module configuration page.
To solve the other issue, I simply unpublished the the payment option we didn't want. Again though, these settings changed when we upgraded. We had not changed them ourselves.
Payment methods don't publish themselves after an update/upgrade so be sure to have your payment method unpublished.