I had the same issue on an IPMI KVM connection (both via web browser/Java and Supermicro Windows IPMI app)- when installing FreeNAS, the keyboard stopped working once it booted the OS for installing. The solution, at least on that board (Supermicro X9SRI-3F model) was to make a small config change in the BIOS related to EHCI and USB. Per my notes, the specific settings that may be relevant are below.
AMI Bios 2.12.1236
"Advanced" tab
All USB Devices = Enabled
EHCI Controller 1 = Enabled
EHCI Controller 2 = Enabled
Legacy USB Support = Enabled
Port 60/64 Emulation = Enabled
EHCI Hand-off = Enabled
Troubleshooting process -
Java KVM on a separate PC,
https://IPMI-IP-Address; Load FreeNAS 9.10 ISO via KVM CD
the KVM keyboard worked fine to setup BIOS, so the core functionality of IPMI worked (not a hardware issue). Boot drive set only to KVM CD.
The keyboard stopped working only after the OS started, and the installation screen stopped at the point user input was required.
I tried plugging in a physical USB keyboard while viewing the Java KVM, and the physical keyboard worked fine.
After a quick search (my search was not well documented), I saw a reference that suggested the Java KVM emulation may require legacy USB support, so I searched the BIOS settings, and made the settings above to ENABLE (not set to "AUTO") the options to support legacy USB. Upon reboot, I was able to use the Java KVM keyboard.
The only other USB devices on that FreeNAS server are the mirrored boot drives, which work fine with these settings.
At this point, my guess is that there is an issue between FreeNAS/FreeBSD kernel and the BIOS "AUTO" settings for Legacy USB support. Since it is trivial to force BIOS to support legacy USB, this seems to be the optimal resolution at the current time, but may be worth rechecking if someone on the FreeBSD/FreeNAS side is making changes to the USB driver, such as when FreeNAS changes to a new kernel.
This solution may not apply to every motherboard/BIOS, but other BIOS programs may have some way to force Legacy USB support to be enabled, which seems to be the general resolution.