1/ ARP - the two devices are in the same subnet, therefore the switch is not using ARP for this communication, just passing frames at Layer2 between them.
--> check the ARP table on the server itself during an event
--> initiate a ping during an event
2/ MAC-address table - if a switch receives a frame with a destination MAC address that is no longer in its MAC address table, it sends the frame out all ports except the one it received it on, so the frame will be successfully transmitted whether it is in the table or not.
--> Double-check the Nexus switch doesn't have some weird feature that disables Layer2 flooding.
--> put a static MAC-address in the switch MAC-address table to rule this out
--> Are there any aggregated links between the two devices?
Sounds more like one of those NICs that goes into power saving mode, although the second ping you describe would seem to rule out a problem on the ISS server. What software version is on the 3300?