Cool, glad we got that odd mystery figured out.
For the record, if you have duplicate MACs assigned the same IP addresses on the same network, it is expected that there only be one corresponding record in the ARP tables... the endpoint has no way of knowing that duplicates exist.
The only direct evidence is weird misbehavior like what you saw, or, if you have nice managed network switches, you might get an alert from those.
The network switches connecting the machines (whether physical or virtual) will be continuously updating their notion of which port actually "goes to that MAC" according to which of the duplicates most recently transmitted through that switch, so packets destined for the duplicated MAC address will go to one machine or the other, seemingly at random. The hardest-hit victim of this is TCP, since the TCP connection state information can have a long lifespan and will only be known to one of the two duplicates...
Cheers,
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Darius