When recording your new audio track have you a) created a new audio track in the arrange b) selected that audio track in the arrange (highlighted it) and c) if it is a track from an audio microphone are you doing it with headphones on?
Your merging problem sounds very odd and forgive me if my question is a bit patronising but I am taking this back to the VERY basics.
Thanks for the response. I know it sounds ridiculously basic. Yes I am creating a new track and selecting it. The third track appears in the arrange window, but changes to, for example, the third track affect the 1st. Doesn't matter if it's a 1/4 inch guitar or XLR mic. Yes I'm listening to the headphone output from the Duet.
I think the fundamental problem is my not understanding something about mono/stereo, or prehaps input and output settings. I just can't seem to find the appropriate controls/settings.