This bug bit me today, so I'd just like to leave this here and make people aware that it's still an issue with 5.1.7.
Symptom: Using sequencer mode, assigning a part to one of the analog outputs 1 to 3 has no effect and the part is still sounding on output 1.
Workaround: Switch to single mode and back to sequencer mode. The analog output assignment is now in effect.
This is especially annoying when the Virus starts up in sequencer mode since it means you'll have to apply the workaround every time you turn it on.