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Hi mark I had this exact same problem months ago when we did a week in an alternative tuning and even resorted to doing what you said finding the note on another string and tuning by ear as my tuner would only seem to let me tune eadgbe automatically. I found an old tuner which I had and this allowed me to tune a note so maybe it is your tuner there’s plenty of apps where if you pay they have the alternative tunings built in. I have a new guitar now that has a built in tuner which is really good it lets me tune any notes. Someone might have a better answer as I never found a solution with the tuner I had but that might just be my inexperience also.
