Hi HarryT,
I followed the guide here:
http://cc_faq.multipie.co.uk/index.php?solution_id=1094
I had calibre companion setup to copy all my epub files into one directory. I had to delete everything and then set calibre companion up on android the way that they suggested - i.e so that each epub file is in it's own directory (under author/book title/ ect). That sped things up a lot!