That MP3 you linked to sounds exactly like the powerheads in my aquarium do when they get air in them after a maintenance cycle until I get all the air out (side note - they are completely submerged 1 foot down in 80 - 90 gallons of water). That sound is from the impeller.
As Brad said, excessive back pressure can also cause impeller rattle. From what I've seen/read a fair number of systems in Europe are pretty restrictive. 3/8" is "large" tubing and 1/4" tubing isn't uncommon. Some of the water blocks look to be pretty restrictive too.
I've also noticed on my aquariums that higher back pressure makes it much harder to get all the air out of the impeller cavity. With high back pressure the air bubbles tend to stay attached to the impeller.
To see if it is either air or too much back pressure, put the pump in a large container of water (15 liters or so) with the pump sitting on its end so that both intake and exhaust are "up". Don't have any tubing attached to the pump. Start the pump and gently shake it for a minute while it's running (shaking helps to break any air bubbles loose).
If the sound goes away, turn off the pump and then add your tubing to the pump's outlet (try to attach it without removing the pump from the water). Then turn it back on and see how if the sound returns. If it doesn't, then grab the end of the tubing (output end) and "pinch it" down as far as you can to increase the back pressure on the pump and see if the sound returns.
For a final test if you make it this far without the impeller rattling, connect the tube to the inlet of the pump, making sure you don't get any air in it. Repeat the "pinch down" of the tube with it running.
I very seriously doubt the magnets have anything to do with the issue (and in thinking of how a mag drive pump works - can't come up with anyway it even could cause impeller rattle).
Note about the back pressure causing impeller rattle - when the flow restrictions are too high, the impeller can't rotate at the same speed as the driving magnetic field. The impeller ends up starting to move forward, but because of its slow speed due to the back pressure, it ends up "falling out" of its current magnetic field lobe. At that point it actually reverses direction until the next forward driving lobe starts moving it forward again. To envision what is going on, think of it like you have two permanent magnets, with one alternately being reversed in direction. This will alternately push and pull the 2nd magnet. This alternating motion is what causes the rattle you hear in those cases.
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