As you have mentioned yourself, the problem is with AR9331 [internal] hardware and it's unlikely that anyone outside Qualcomm can do anything to fix it. We did however spend a lot of time and resources debugging this and have found ways, which overcome the problem 100% of the time not only for us, but for our clients too. The solutions are following:
1) In full-speed mode - use software patch.
2) In high-speed mode - use Microchip USB2640 hub. Other hubs that were tested but did NOT work: NEC 720114, Genesys GL850G.

Hi,

We use FE1.1S 4 port hub with two FT232 devices on board with the stock firmware without problems. I'm curious to know if your USB serial devices are chips on your PCB or on a cable from a USB socket?

Regards,

Liam.