From another forum:
"Apparently PayPal recently updated their systems, which caused the double charges in shipping. There is no button or selection to turn off shipping. What users will need to do if this occurs is go into Shipping Calculations and delete all calculation methods. When PayPal migrated my account to their new system, they inadvertently created a default shipping calculation. It wasn't obvious on how to turn it off since I didn't create it in the first place.
To turn off shipping, users will need to delete any shipping calculations that may have been created when PayPal updates their system."