Hi,
It will only autopaid the new invoice if you have overpaid their(customer) one of the invoices or some of them. Excess/floating payments automatically pay the incoming invoices, it also possible that you have deleted some of their paid invoices.
You can run their statement to see if the total invoice and total payments are balanced, in case the Payments total are higher with Invoices total yo will need to delete some of the payments.
For the emailng issues ,please reenter your mail host,email and password then click ok and please also check within your antivirus/ firewall/networking if blocking the outgoing ports 25, 465, and/or 587.
In case your still having issues please go to http://www.nch.com.au/support/index.html