Hi Jordy,
I think I spoke too fast…
I checked again at the main site of the WPMU installation and I now see that there are media reported that are in fact belonging to network sites.
Maybe you should check this further.
The usual (default?) media folder structure is that the main site has its media under the /uploads/ folder – the same as any other standard WP installation – while all other network sites have their own folders under /uploads/sites/ and each one with a new subfolder taking the network’s site id number: /uploads/sites/1/, /uploads/sites/2/, /uploads/sites/3/, etc…
I don’t know how you may set this up but probably with something referring to the each site’s ID number.