We are having discrepancy between esxtop and client performance chart too.
We have some machines showing about 150 receive packets dropped in the network performance chart. But esxtop says 0% dropped for the same machine.
I've found an article with some information about changing failover settings in distributed switches (http://www.null-byte.org/vmware/random-packet-loss-with-vmware-esxi-5-1-virtual-machines-using-vcni/). We do not use distributed switches, but made some tests changing failover order, and the number of receive packets dropped went down to about 10, but started to rise slowly again.
Even when changing failover order, there was a discrepancy between esxtop (0%DRPRX) and the performance chart.
Looked KB:1010071 too ("The output of esxtop shows dropped receive packets at the virtual switch"), but we have no dropped packets at the virtual switch, only on the virtual machine.
If we review the information in the guest OS (RHEL 6) with 'ifconfig', there are no dropped packets. We have one vNIC and two IPv4 addresses, one in eth0, and the second in eth0:1.
We have upgraded our infraestructure to ESXi 5.1.0, 1117900, and reinstalled the vmware tools using --clobber-kernel-modules=vmxnet3. But the issue still persists.
Does someone have any clue?