The situation is as follows:
A customer places an order and gets an email from Paypal saying: Your order number is 1000001
In the system we don't see 1000001 we only see 1000002 with the same transaction information that we see in paypal and from the transaction email from paypal.
So Magento is linking the correct transaction to the order numbers but appears to be allocating two order numbers but only using 1.
Has anyone seen anything like this before?