Do the Opportunity Forms in your account have the Store Form with Record option enabled?
An Opportunity record created and set with a form that has the option enabled has a reference to that form stored in the record and will always use that form regardless of the preferred form. Disabling the option does not delete the reference to the stored form that was last saved with the record.
Note: The Standard Opportunity form has the option enabled thus, it will be always used for records created where it was set unless the record is edited and the form is changed to another form with the option that is also enabled.
The solution for the system to respect the Preferred Form for new records moving forward is to disable the option on all Custom Opportunity Forms and inactivate the Standard Opportunity Form.