If you have a good relashonship with your agency then it should be not problem. Just remind them they make a fair bit of cash from you.
But they may have however billed the client based on the fact you were not VAT registered, even though there bill would have incured VAT (assuming they are registered, which they will be)
Have a look at you contract, how is the rate expressed is it say something like £45 + VAT/Hr or just £45/Hr. If it does not detail the VAT then I reckon they may tell you to poke it as they assumed it was £45 including the VAT.
Remember though your contract is generaly with the agency, they are the ones who pay you, not the client. So its upto them to be kind to you not your end client.
This really is noddy stuff, as a director of a company you do have certain responsibilities !!!!
Bazzer
PS Edited to add BR is right as an IT contractor generaly the FRS scheme is the way to go, unless you are a geek and buy lots and lots of computer equipment for you work.