For the 40GbE side I have an Arista DCS-7050QX as the switch with both nodes using Chelsio T580-SO-CR Ethernet cards with FS modules and fiber. No jumbo frames where turned on. I didn't dive too much into what was going on with the 40Gb as that was just another layer of complexity that I shouldn't be sorting out just yet.
10Gb side is an Unifi US-16-XG switch, no jumbo frames. The cards are an Intel 520-DA in the ESXi node and the W2k16 server is using the onboard Intel 540 (10G base-t). This might be where a lot of the problems are. The unifi switch is showing 10Gb speeds but those ports are known to be hit or miss. I don't have a spare 520-DA card at the moment to test it, but my feeling is that it might help.
10Gb side is an Unifi US-16-XG switch, no jumbo frames. The cards are an Intel 520-DA in the ESXi node and the W2k16 server is using the onboard Intel 540 (10G base-t). This might be where a lot of the problems are. The unifi switch is showing 10Gb speeds but those ports are known to be hit or miss. I don't have a spare 520-DA card at the moment to test it, but my feeling is that it might help.