Thanks very much for posting your fix! I have been plagued with the same issue and same PayPal error over the last few months so bit the bullet and switched from PayPal Standard to PayPal Express. The issue seemed to go away but this week one in 4 orders has been a double order and like you one of each of the orders had no PayPal transaction details. At least under PayPal Standard I just had duplicate orders but only one payment but with Express I was getting two payments as well.

After some testing and troubleshooting the problem seemed to be a large delay (up to 30 secs) between clicking on 'Confirm The Order' and being returned to the account to download. I initially assumed it was PayPal related but then found that free orders could be very slow as well:

01/06/2015 01:51:55 - /index.php?main_page=checkout_payment (0.166s)
01/06/2015 01:52:02 - /index.php?main_page=checkout_confirmation (0.243s)
01/06/2015 01:52:27 - /index.php?main_page=checkout_success (0.235s)

Having switched from smtpauth to php the checkout is now instant so hopefully the duplicate order issue will stop.

01/06/2015 04:01:26 - /index.php?main_page=checkout_payment (0.182s)
01/06/2015 04:01:29 - /index.php?main_page=checkout_confirmation (0.186s)
01/06/2015 04:01:32 - /index.php?main_page=checkout_success (0.179s)

I had noticed that I occasionally wasn't getting order confirmation emails so I did wonder if it was email related.

I use GMAIL as my provider and the emails are still coming through but are there any downsides of using php instead of smtpauth?

Although I wasn't hopeful it would fix the issue at least this has forced me to start looking at upgrading (1.3.9h > 1.5.4) so I am well down the path to achieving that!