I had a similar problem last week when upgrading my home FreeNAS system to a Skylake H170 board. Moving the FreeNas system USB 3 stick to the new MB which only has USB 3.0 external ports the boot got stuck at the mountboot prompt regardless of BIOS settings. Tried to connect to the internal USB 2.0 header instead. No improvement. Put in a PCIe USB 3.0 card and moved the USB stick there. This did the trick and the system booted without problem. However, even after completed boot no USB devices can be connected to the on-board USB ports.
Looking at the postings at this forum and elsewhere the poor functionality of FreeNAS when it comes to USB 3.0 support is becoming an increasing problem as USB 2.0 is becoming a legacy specification and new MBs will not properly support it.
I believe a push from the development team to resolve the USB 3.0 issues would be gratefully appreciated by a lot of users and secure the ability to use USB for the system installation