Its very easy to explain - Waterstones are a bunch of theiving b*******s.
Their web site is awful to use, their selection is rubbish, they only respond to emails telling them so with standard 'thank you for using waterstones, we are working on it...' emails, and they want to charge as much as they can get away with (an yes, there is vat payable on ebooks).
The books that I have purchased (and 90% of my ebooks so far that I already own in hard format have come from the dark), I have purchase through ebooks.com - its at least half the price of waterstones and you can actually find books on their site.