Unfortunately, this didn't resolve the issue. But hey, at least now we're running fiber like a real datacenter.
After lots of troubleshooting and chancing upon a forum post, I discovered that there seems to be a bug in the BIOS for the X10SL7-F motherboard in my FreeNAS server. Changing a BIOS setting fixed the issue. Thank god for people who come back to their forum post and reply with an explanation of the solution.