I am having the same problem. I ship to 2 different countries and each has 2 shipping methods (1 flat rate + 1 free shipping) for customers and 2 (1 flat rate + 1 free shipping) for wholesale users. I have configured all 8 profiles but when trying to check out it still shows both shipment methods?
Are there any hidden profiles that need to be configured? I also tried to do the debug / cache trick but that didn’t work either and a hard reset/icognito mode.