Thanks guys. The windows are fitted now and it's only when I've received the invoice after asking them to zero rate it (which they didn't challenge at the time) that they're now insisting on VAT. We did separate the supply and fitting so I should be okay reclaiming the supply costs and I'm still fighting the issue asking for the grounds, rationale and contrary guidance that they're relying on. I think your right jamiehamy in that they're just going for the safe option at my expense.
I can't go into too much detail about the company that supplied the old windows as we have now settled and there was a gagging clause in the settlement agreement where I can't publicly name and shame or review them. I had to accept that to get the refund. In summary though, the problems I had were around severe, and I mean severe leaks. Sash horns and other trims falling off (they were PVCu sliding sash windows). Chrome furniture rusting really badly. Exterior seals perishing. All of this happened within few months. If you've got some specific issues with a company, I can tell you privately whether it was the same one (it was a biggish manufacturer) and how I resolved it.