We are now using the latest official SDK libraries, which are completely different to the old ones we had. We will base things on the official USB stack, and if that has problems as well we will seriously give up on these boards.
If it works, we’ll see if it can be used at least for reliably reading DD disks. HD is less likely - it may just be too slow as clock speed is limited when USB is active and we don’t have enough RAM onboard to read a track directly. Most people would probably have gone for a more capable (and much more expensive) device by now, but we will see how we go.
Anyway, here is the problem with some boards board explained in detail: http://www.at91.com/samphpbb/viewtopic.php?f=15&t=4745
It’s basically a direct copy of an early non-USB compliant design as was suspected. Luckily enough, the only version where that hardware problem is fixed is the board we ordered.