duplicate orders using cybersource module

I am running an older version of the cart 1.2.6 and the site process around 10 to 30 orders a day. I started getting duplicate orders about three months ago, after a php upgrade I think. I am using cybersource as a payment gateway.

I also get duplicate charges every once in a while where an order is charged twice, even with prevent duplicate orders set in cybersource.

I have been working on upgrading the site to 1.3.8 (not a small feat by the way) and was hoping that would solve the problem, but after reading this thread I am beginning to wonder.

Has anyone found the problem with this yet?