I'm afraid that this is the most significant evidence that confirms the hypothesis that Paul Stoffregen made during the test phase of the Due: we are facing a Snow Leopard bug in the CDC driver implementation that has been fixed in Lion only.
At this point, these are my thoughts:
Quick and dirty (temporary) solution: provide a way to implicitly set the device class code at runtime, when needed. In this case the workaround could be activated from within the sketch, from example reading the logic level on an input pin.
Trace the USB communication between the Mac and the Due and look for some kind of fingerprint that can tell us when the host is a Mac OS 10.6.8: this seems unlikely, but why not to try.
Provided that this could be a solution, develop a USB driver for the Due, but, as Louis Davis pointed out, this is hardly worth the effort...
I'll do some test on 2) within the next weekend and let you know.