Is there anyway to stop the Auto responder emails being sent to attendees junk email folder?

I see  you  already setup SMTP from your hosting provider: http://www.jotform.com/help/244-How-to-Setup-SMTP-for-a-Form, if the autoresponder still arrives to Junk's Folder, you can try using SMTP from Mandrill: http://www.jotform.com/help/236-How-to-use-Mandrill-to-Send-Emails-From-Your-Own-Email-Address

Let us know if you need more help, we will be glad to assist you.