I didn't observe similar problems with C III yet, except for a customer, who tried E144 package with floating exposed pad. Regarding unusual "special" configuration circuits, e.g. pulling nCONFIG high, as long as you do't know the exact internal circuit connected to the pins and their operation, I would avoid these. You can place a decoupling diode and revert to the Altera suggested circuit. But you are most likely right, that this isn't the cause of problems.
I wonder, if the ferrite bead without decoupling capcitor may cause unwanted ripple or even overvoltages on the device side supply node.