The fact that the invoices are made out in the name of the builder is likely to be viewed by HM C&E as evidence that the supply was to him and, if picked up during a visit, they would likely refuse any claim to input VAT.
There could be an argument that the builder was collecting purchases made on your behalf and that the invoices are therefore incorrect. I should think that HM C&E would resist that argument.
The have been tribunal cases whereby the chairman has accepted that a registered person can reclaim input VAT even though invoices were made out to other parties. You could reclaim the input VAT on this basis and accept the fact that if you receive a VAT visit HM C&E are likely to assess you. You could then decide how far to pursue any argument with C&E.
Regards
Paul Taylor
0121 778 4299
http://www.vatease.co.uk/