I seem to remember something like that happening in a v4.x store, it has been a long time so I can't remember why....
Have you made sure all of your store's modules are up to date?
Have made sure to set all settings in the shipping settings manager?
What are the settings in your Shipping settings manager?
If all else fails, I would suggest doing a fresh install of the cart. Set it all up so that the default cart is working.
Then, slowly start applying customizations and adding new products. If it does it again, testing along the way will help narrow where the problem is occurring.
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God Bless!
Bonnie - AgoraCart Moderator
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