simtrace2 firmware fails to zend zero-length packet on IN endpoint if transfer size == wMaxPacketSize
wMaxPacketSize for full-speed devices such as the SAM3S devices as per the USB specification is 64.
Similar to what's known from DFU transfers on control transfers, we also need to send zero-length packets on bulk endpoints whenever the transfer size is exactly a multiple of the wMaxPacketSize. See USB 2.0 Specification Section 5.8.3 Bulk Transfer Packet Size constraints.
This is not implemented in the simtrace2 firmware and I just hit this reliably when a 50 byte APDU payload was transferred (which tother with our headers added up to 64 bytes).