I made a booking with Booking.com for a few days away in Barcelona in Oct, it was a non refundable one, quoted in Sterling but charged on the confirmation in Euros. No problem there, but when do you think they'll take payment? Unless the Euro is gonna nosedive I'd rather have the booking paid up in full.
I have used Booking.com many times. Usually when it is not refundable you're charged very soon after making the reservation. No offense, but are you sure your credit card has not been charged ? You can always send your booking reservation no. to them and ask.