Regarding the four possibilities that were mentioned:
1. softnet backlog: no idea what that is
2. Unintended vlan tags: Quite unlikely, unless you had connected your system to a trunking port on the switch.
3. Unknown protocols: Quite unlikely.
4. IPv6 frames your not supposed to be getting: How would this happen?

For my part, I think this is just a congestion issue... perhaps at some part of the day (or time in the past) you got a burst of NAS-related traffic higher than your system can handle.

Dropped frames are not necessarily a bad thing. The traffic gets too high... the receiving end drops some frames... TCP realizes it needs to slow down... the data transfer gets throttled back to reasonable rates. 2% loss does seem rather high, but if it is a busy server... Maybe you'll want to configure some kind of network or application-level logging system and find out when exactly it is the system is getting hammered the worst.

Yes, it is problem. The question is whether the drop is harmless or critical. There are four reasons in list. If you want to know what reason cause the drop, it could take you some time to find out. You can check the sniffer result, about IPv6 packet, VLAN tag and IP protocol. If there is any this kind of packet in sniffer result, you will know reason. If no, it could be buffer full.

stateless, I have isolated the NAS, network device, and PC to be doing nothing but the test. There are no VLAN and IPv6 setup.

How can I check buffer is full or not?

Don't ignore testing. If you use testing tool to test something, testing tool could generate unknown packet, such as unknown IP protocol and unintended VLAN.
How about IP protocol? NAS access could use layer 2 packet.
It is hardly to check buffer status because so many buffer in software module.

For me the resolution to this problem was noticing that ESX reassigned ethX across the virtual NICs. After reassigning the port groups, all was well. I believe this was due to a vmxnet NIC being added after 3 E1000 NICs were added and configured. The vmxnet adapter took eth0 and shifted everything else.