Thank you for contacting Intel.
The 2 ports of X540 Series Adapter can support 10Gbps. With regards ports' speed settings, you may either use auto-negotiation or force the speed at 10Gbps.
If the remote device connected to Port #2 is also running 10Gbps, then Port #2 should also run at 10Gbps.
Feel free to contact us again if you have further questions.
Thank you for responding.
Unplugging/re-plugging the "slow" connection fixed the VMware hosts, but not the Thecus, I suspect an obsolete driver.
For the time being, I'll pursue resolution with Thecus customer support.