If you went via a 'clean' browser, I wonder if you didn't get your Booking.com "genius" discount from not being logged in? This specific discount has never been an issue with also getting the Avios awarded.
And I frequently use estore with Booking.com as the 8 Avios/£ is a decent rate, but have not yet seen a price discrepancy (SOP for me with all 'cashback' type sites is always to check the standard pricing 1st!)