Did you take a look in dmesg for the new setup? The old one clearly was catching spoofed packets:
ixgbe 0000:03:00.0: eth0: 1 Spoofed packets detected
A couple of things - are you doing this for eth1 as well? Since you are bonding you need to do it for both devices. And I see you are calling setting this for VF0 -->VF63, however the 1G devices only have 0-->7.
thanx,
Patrick