Okay well the way you explained how you set it up led me to believe you where using an old version cause you do not set payment in payment options anymore in 2.5
Well remember if your using multiple usergroups both need to be set to allow payments.
When a user belongs to multiple usergroups the program will assign the best possible permissions scenerio so if say a user belongs to a group that allows payment and one that does not have to pay then they will not have to pay.
Make sense now