I don't have access to cron on my customers account so I have installed the plugin.
In my tests I'm using the paypal api payment method and emails are not being sent even if the payment shows as confirmed in the invoice list.

EDIT: Apologies, I've just figured out how it works now...goes out every 30m...I expect that's in the manual!

One thing though the automatic email that went out used the delivery note email template with the invoice attached even though I have DN turned off. Why is it doing that and how do I stop it.

My workaround for now is to copy the invoice email template contents to the delivery note sections but I would like this to function properly.

The body for email with invoice is taken from VM Invoice / Global Configuration / Mailing / Mail Body field.

You misunderstand.

The issue is:

Even with Delivery Note section disabled.

When auto email is sent, it arrives with "Delivery Note" as subject.
With Delivery email contents and Invoice attached.

Then update the email subject for the invoice email: Mail Subject field.

No, I've had to change the email subject for the Delivery Note email to Invoice and change the content of the DELIVERY NOTE EMAIL to read like it is for an INVOICE.

I have a workaround...you have a commercial application that doesn't work as it should.

That was a bug in mailing configuration, thanks for reporting. Until fix is released, try to disable also "send both" option in delivery note configuration. That should turn subject & body back to normal.