Make sure your nic settings are matched to the switchport settings. If you have your nic set as auto then the switchport must be auto for speed and duplex. If you hardcode the nic to 100/full then you must hardcode the switchports to 100/full otherwise you have speed/duplex mismatches which cause errors and slow transfers.
You need to set a baseline here as in theory you should be able to reach almost 100Mbps, however the servers (and their operating system) are more likely to be the bottle neck. Put an Ethernet cross-over cable between the two servers and hard-code them at 100/Full then run your transfer test. You should then repeat it via the switch, however you will need to reset the NIC settings on the servers back to Auto - I recommend you leave them at Auto when connected to the switch. Once they are connected check on the switch and the NIC utility that they have negotiated 100/Full (most NIC's have a utility to show the negotiated Speed & Duplex).
Once you have the baseline you need to compare it to the results of the transfer through the switch - it should be similar.
We are pleased to announce availability of Beta software for 16.6.3. 16.6.3 will be the second rebuild on the 16.6 release train targeted towards Catalyst 9500/9400/9300/3850/3650 switching platforms. We are looking for early feedback from custome...