well, i'll answer my own question for the record.
I just spoke to one of the incredibly helpful people at the Mouser UK office and they told me that they used to have a lot of issues with Fedex randomly charging people for VAT admin fees etc. Because of this they now add the VAT in their credit department in the US as your order goes through, and for some reason they pay the VAT on your behalf as the order goes through their clearing house in France.
To quote from an email i was sent:
'If you choose UPS then then VAT is added at customs together with an Admin fee. However if you choose FedEx International Priority then we pay VAT as the goods clear in France. If you have a VAT number we can zero rate your invoice for VAT, but if you do not have a VAT number then we add VAT to your Mouser invoice. At the moment the VAT is not actually added at the checkout - it's added as the order goes through the credit department (this is because even people who give us a VAT number - if it doesn't verify then we still have to add the VAT) - but essentially, yes, if you choose FedEx you will see the price of the goods plus any shipping charges due and then our credit department will add VAT. When goods go through customs, it's customs who add the due VAT and they charge VAT on the average cost of the shipping - even if it's free. That is why with FedEx we now bring the goods in through a clearing house in France and then if you pay £12.00 for shipping the VAT is only on that £12.00 not on the 'average' cost of GBP 40-50. You will not then receive any further invoices from FedEx.'