I know brochure prices are guidelines only but we booked to go to Kenya (not going ahead now but that's a different matter) in September at a Thomson shop with Hayes and Jarvis. The price was roughly £5k quoted with £4k if you worked it out in the book or compared it to Hayes and Jarvis online (before the separate "web discount"). We of course cancelled, lost our deposit and rebooked online because they refused to acknowledge that they had overcharged. Hayes and Jarvis have said they have refunded the original deposit to Thomson retail and we should be refunded - Thomson retail say they haven't received it and therefore haven't paid us despite allegedly having the deposit for a month.
As both are Tui group companies, I don't see what the problem is, but obviously they have found one. My advice is to always book direct and online if possible as at least you can see the breakdown quite clearly. (The shop said the difference must be agent's fees - but £1k?)