I eventually found a way to solve the brainstem issue. I can now use the serial brainstem with a serial-usb adapter without any annoying bugs.
The braintem unstable issue (e.g. counldnt boot sometimes, no diagnostic data output) is due to the serial brainstem gets the 5v power from the dsatx J2 port, which somehow make the dsattx unstable.
The resolution is to connect only the TX and RX wires of the brainstem to the dsatx J2, meanwhile connects the 5v and ground wires to the harddisk power cable (I.e. the 4 pins power cable connecting the psu to the harddisk or cdrom), such that the brainstem will not get the power directly from the dsatx J2 port.
By doing this, the brainstem works when it can get the power from dsatx through the power cable, and I can us the brainstem for configuration and real time monitoring. Hibernate upon ignition works just perfect now.