Synology read performance degrades with Jumbo Frames over 6000
Solution 1:
Update the Firmware
In my experience, Synology fixes a lot of issues in each firmware release and the one you're running is nearly four years old. I have not read the release notes, but there seems to be lots of opportunity for a Jumbo frame bug to have been fixed since then.
Test with a Direct Connection
Connect your test machine directly to the Synology (assign static IPs on the same subnet) with new patch cables and re-run your tests. This will eliminate the cabling and switches as well as any other equipment and configuration issues. If the problem remains, run your tests with another computer. If it still remains it's certainly the NAS.
If the problem goes away during the direct-connect test, then try replacing the switch first, then the cabling. You haven't shown the connections so I'm assuming just the TPLINK between the test machine and the NAS.