Chris is correct that there are several factors which can reduce the achievable burst depth and rate. The things he lists are certainly worth checking out.
Just one other point...
>Looking at the manual, p.423, there is a table that is most >interesting - there is a buffer limit for the number of frames >I can shoot before it stops, as in click,click,click...... >click...... click. It gets busy writing stuff to the CF card >I assume and the fps drops to less than I could do manually.
Switching to "manual" (by which I guess you mean Single-frame Release Mode rather than Continuous hgh) won't really improve things - if the limiting factors are the buffer size and the card write speed, there won't be space in the buffer to shoot faster, however you try to do it