well I tried to reproduce your problem and I will admit that I am now confused.
I am running Snow Leopard and iTunes 9.
Earlier this year I had my BS 2 repaired ... so I am not certain of its firmware level and its iTunes/Windows setting.
As you probably know getting the BS2 to switch modes is a tedious three handed process ... and not matter how many times I go between what i think is iTunes mode and Windows mode I can not get iTunes to recognise the BS2.
When I think I am in iTunes mode the BS2 shows up on my desktop as a hard drive configured in MS-DOS (32-bit) mode.
When I think the BS2 is in Windows mode it does not show up on the desktop nor in iTunes.
I think I shall go kick a Windows machine ... sorry I mean 'boot' :-)
PS no crashes along the way, but plenty of complaints from MacOSX about me removing a drive without ejecting it but that is standard/normal behaviour ....
First B&O (1976) was a Beogram 1500 ... latest (2011) change has been to couple the BL11 with the BL6Ks *sounds superb*