In z2 mode the INT bit in $4800 is set. In z3 mode it is not set. In both cases this is before i have initialized the rr device.
The USB module starts up with IRQ-passing disabled. This will ensure safe startup of the Amiga, even if the chip goes wild due to faulty software.
So to me it seems that in z3 mode, somehow this bit is set before any software is run. Basicly what Jens said i guess..
Please send me what you got.. Fun to look at.