Noise source identified!
I feel a little embarrassed actually, the solution was very obvious and did not require replacing the MB at all. A guy from Gigabyte support NL called me on the phone, and said that after hearing the recordings, he suspects that it might be a faulty engine in a case or CPU fan. I disconnected the CPU fan while the computer was running, and the noise stopped immediately. Of course I connected it right back. So now it's just a matter of replacing the Intel stock CPU cooler.
I was so locked on the idea that the UD3R boards make noise, that I failed to look into other, obvious possibilities - a fan making noise? who would have thought?
(though the noise
was far from typical fan noise)
Thanks again Dark Mantis for your help, it's always nice to come across such generosity. Also it's worth mentioning that the Gigabyte support team were very helpful, as well as the RMA technician at Zercom.nl.
Cheers!
Assaf