I'd kill for some advice!

Backgroud:
I'm a Czech citizen with a Maltese wife. Both of us live and work in the UK. I've been here since August 2004 and my wife has been here since May 2004. We've been in a de facto relationship since 2000 and were legally married four years ago. We've just made a joint application for British naturalisation. The Border Agency has written back to us to ask for my Workers Registration Certificate (WRC). I don't have one because neither I nor my employer (which is a large corporation with thousands of employees) was aware that the Workers Registration Scheme existed.
Our case officer at the Border Agency has said that our application is impeccable with the exception of the missing WRC. She has also told us that it is no longer possible for me to apply for a WRC because these cannot be backdated and, as the husband of a Maltese wife, I am no longer required to have a WRC.

Questions:
(1) What will this missing certificate (which I cannot obtain) mean for our naturalisation application?
(2) The case has been referred to a senior Border Agency officer. Has anyone found himself/herself in a similar situation? If so, what happenned in your case?


Many, many thanks,

Kris

 

Anyone? I'd be grateful for any advice at all!

Kris