See page 47 of your MOTU 2408 manual ( on the Windows PC side ). The
section called 'Interface Options' will tell you that when none of the three
banks are set to analog, one of the three banks will be mirrored to the
analog bank you select. ( bank A by default )
I suspect that you may have analog outputs 1 and 2 of your 2408 connected to
analog inputs 2 and 3 of your Nuendo 8. If not I'm not sure what is going
on.