At the moment, when you create invoices based on a PayPal import, we know that only one line is imported (blame it on the paypal API .as normal, rather than using the correct API...)
Anyway, that first line always has the VAT rate set to 0% by default, even if you are a VAT registered business.
Surely it would be better to default to the seller's standard rate of VAT (or have a means of specifiying the VAT rate to use on paypal import).
At least then, there would be a chance that your VAT amounts are correct (except for sales outside the EU)