Erratic Double Orders after upgrade

This cart is double charging - creating 2 orders per order in a very erratic manner. It does not depend on which payment method or shipping method. It also does not happen all the time. For example

customer 1 yes
customer 2, 3 no
customer 4 yes
customer 5, 6, 7, 9, 10 no
customer 11, 12 yes

Just upgraded the cart to 1.3.9h and there aren't many customizations to the files.

The 2 payment methods are paypal express and paypal pro. Those were removed and reinstalled (the client did it).

If both of those exist, is there an order they need to be removed and reinstalled? I don't see how anything can cause such erratic behavior but obviously we have managed it.

delia:

The 2 payment methods are paypal express and paypal pro. Those were removed and reinstalled (the client did it).

If both of those exist, is there an order they need to be removed and reinstalled? I don't see how anything can cause such erratic behavior but obviously we have managed it.
No. As far as default core code goes, there's no special "order" other than the fact that Pro won't let you install it if EC isn't installed. But that has no bearing on double orders.

Suggestion 1: http://www.zen-cart.com/wiki/index.php/Troubleshoot_-_Diagnosing_Obscure_Issues

Suggestion 2: Upgrade to latest.

I uploaded all default files again and we reinstalled paypal mods. Now I find that part of the problem is when the customer hits the finalize order button, the message:

Email Error: Could not instantiate mail function. Please check Admin->Configuration->Email Options->Email Transport.

appears. But the emails are working fine with no problem.

Using php as transport method, and as I said it is working.

I'm thinking the double orders was due to people refreshing that error message or trying again thinking their order hadn't worked.

php as transport method can be unreliable. SMTPAUTH is the most reliable approach and most compatible for all modern traditional webservers.