Thanks everyone. There is a definite drop in organic traffic and our normal presence on page 1 is 7 or more pages in the hole now. Haven't had notification of a penalty, though it feels like it.
Cleaning up some technical seo problems at the moment with sitemap structure etc. I tend to agree with Andy... if it walks like a duck....
Open site explorer is where I will start. Thank you. I will try Majestic if i need to dig further.
Really appreciate the responses.