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It's just two switches.
Server 1
10Gbe
ubiquity switch
10Gbe
qnap switch
10Gbe
server 2.
I'll ask some basics:
Is the ubiquity switch the flex-xg? Make sure you're using the 10G ports as the poe port is only 1G.
I'm assuming all the ethernet cables are rated for 10G?
Are any of the switches or NICs manually configured to negotiate at a lower transmit rate?
That's all I've got, good luck.
So then it doesn’t work across the ubiquity switch just to double check? If so, you will need to enable jumbo frames on that for sure and it is not enabled by default and that could also explain the throughput as it is having to fragment then defragment the frames to cross the switch or iperf is using MSS to determine that it can only send 1500 byte frames, your slower speed is about line rate for 1500 byte frames no matter the speed of the actual link.
ETA: you can verify this by pinging with a large size and setting the “do not fragment” flag, so something like ‘ping -s 2000 -M do ip.addr ’ on Linux, windows uses different flags.