Managed to get it working but not sure why its different.
I was levelling a second character and thought to make it easier I would send the character all the stuff from my main and just level that so I paused the bot, switched char and sent the mail. I got called away from the pc and when I came back just unpaused the bot instead of switching back to the second char. Miraculously the bot ran and handed in a quest. From this point the bot runs fine even when stopped and restarted etc.
Must have been something out of sync somewhere.
Thanks for your help guys