Auto Focus Issues with Canon 1D Mark II

I seemed to have some difficulty focusing with the ID Mark II today which I have never experienced before so I ended up using manual focus for most of the time which is not ideal. Auto focus seemed fine with a short lens but as soon as I mounted the 200L or 300L I lost auto focus, even without extenders, which is not normally the case as the 1D cameras can autofocus with extenders. I am not sure what the cause is so will have to investigate further. It is a shame as many of the pictures I took today, of the kingfisher at mere Sands Wood and the Avocets at Marshside, are not as sharp as they should have been. Those I took with the 5D are fine of course but although the 5D is great for sheer image quality it is not quite fast enough once extenders are added, for catching a kingfisher in flight or avocets playing. I did get some nice shots of some swallows nesting on the roof of the hide though!