Valuers are used to looking at the potential within a property, was he aware that you were in the process of doing it up? he may have been well aware, but still didn't think that it had good resale prospects.
mortgages are just so much harder to come by now and lenders are being increasingly cautious. It may be worth contacting the valuer to see if he had taking into account the state of the property at the time of the valuation. Many lenders will only use a particular group of valuers, so they may not be interested in a 2nd opinion, but it may be worth asking them, or simply shopping around to see if you can get a mortgage elsewhere.