We went through EMC with a similar product with the BBBI, and didn't have any issues.
We developed a cape for the beagebone black industrial by element14 and we were going to use it as data collector for our applications.
When we sent the BBB industrial to laboratory for EMC tests as requested for the CE marking they informed that there were several radiated emissions that were out of the limits.
The industrial BBB is provided in a box with FCC and CE marking, so I guess element14 has the CE certificate. Can you please provide it so we check it with our laboratory. We provided them the CE certificate of the Beagleboard page but the emission measured by our laboratory are completely different.
Please provide us as much information as you can so that we can make tests again and go forward.