The Issue:
A common issue regarding Wholesale Role/Shipping Method Mapping is when you have multiple shipping methods with the same region. If you have that setting, the shipping zone in the higher order will override the other one and this causes the shipping method mapping to not be applied properly.
For example, you want to have a Flat Rate shipping method for retail customers and Free Shipping for wholesale customers in the United States.
The Solution:
Instead of having them separated, combine all the Shipping methods with the same Region as shown in the picture below. This way, the Wholesale Role/Shipping Method Mapping can be applied properly.
For additional reference, please visit the link to learn more on How To Restrict Wholesale Customers to Using Particular Shipping Methods.
