I've been trying to track down the cause of this myself. The problem I'm having is that there is no documentation available for the Marvell 88E8001 Ethernet controller.
I've found that if I modify my I/O device to insert a 1 ms delay between receiving the command frame and sending the response frame the issue goes away. This leads me to believe the response (from the device without the delay) is arriving during the servicing of the transmit interrupt and the response frame interrupt is somehow being cleared.