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When the flatrate module is enabled and a default shipping flat rate is entered, you can override this value on a per product basis. To revert to the default shipping rate the text in the box "Flat shipping rates" says:
"Override the default shipping rate per product for each flat rate shipping method here. Enter -1 to revert to the default value."
This is wrong. After entering -1 there will be a shipping rate of -1.0000 € (or whatever currency you use). Thus the flat shipping rate for an order will be deducted by this 1 € if that product is in the shopping cart.
The correct handling is to clear this field when you save the product. An the text should read something like this:
"Override the default shipping rate per product for each flat rate shipping method here. Remove this value to revert to the default value."