I've been working with it already, the marks didn't show at 5.6 which I usually shoot at so I could use it for a couple of jobs yesterday. Thanks though, it was worrying thinking that you've totalled your new 1Ds that you've taken a loan out for, on the first day! I've never seen marks like that on my 10D which is why I panicked.
I got back from the shop and decided to see if the pro had done the job properly, I knew that he hadn't shot any test shots with it. The first frame had a black opaque mark covering 10% of the sensor in the corner. Thinking that he had just swept all the dust into the corner I phoned up and said I was bringing it straight back. My wife told me to try a different lens, I put another on and now the mark was in the middle of the frame, the next shot didn't have it at all.
I activated the sensor clean, pointed it at the floor and banged it on the back a few times. A half inch by quarter inch piece of flaked black paint fell off onto the floor. How it got in there I have no idea but it really confused me...