Sorry for the delay in responding. Found 1 entry in the table(jos_wp_user_roles) but changing it hasn't helped my login issue.
I think the best option for me now is to totally uninstall it and initiate a fresh install. How do I do that so that the installer creates the tables during the install process?
OK, found some more jos_ entries in what was jos_wp_usermeta
Changed all these too although like the other entry above, they relate to tables that aren't in my system such as jos_wp_user_user_level & jos_wp_user_capabilities.
I checked against the tables in a standard Wordpress install and these tables aren't present there either. I imagine they're some sort of virtual table or something?
Oh yeah and changing all these to my new prefix didn't fix my issue.
OK, I created a new super admin to see if that would get me access and it did. I then realised I had also changed the SuperAdmin User ID using the Akeeba Admin Tool. This creates a new super admin with a new random ID and changes the login of the old super admin and disables it. It seems this doesn't get sync'd to WP(can't change the logins in WP). When looking in the list of users for WP, I had two users with login "admin". I deleted the one I didn't want and bingo, back in business.
Definite issue there with Akeeba Admin Tools, maybe useful to have a warning somewhere. I'll drop them a line too, they may wish to provide a warning to their users too.