I'm using 1.3.8a and Website Payments Pro.

PayPal orders are completing perfectly, they show in admin, generate all the correct emails etc. The only thing that is not happening is that the items purchased are not being deducted from the inventory.

Subtract Stock is set to 'true'.
The auto-return path is set to checkout_process

For some reason when I place a test order using the credit card field 'my' orders do reduce quantities correctly.

I'm at a dead end on this, and would appreciate any suggestions or advice.