Thanks for the replies.
The connect to itunes feature is optimized for iBooks though right? I much prefer the kindle app.
You were right about converting the files again. I changed the author name to 'Ellroy James' and converted once again. It now appears in the kindle app as 'Ellroy, James'.
The only problem now is my Calibre library looks a bit ugly with 'Ellroy James' in the author column