If note 1’s voltage is set higher than note 2’s and note 2 is higher upthe keyboard than 1 it will scale the wrong way, imagine a graph of the scaling that you are setting.
Can op confirm he is doing this in order (e.g. no going back and adjusting note 1 after setting note 2):
Setting c3 for note 1
tuning voltage 1 to correct voltage for c3 whilst playing a c3 from the sequencer
setting c6 for note 2
tuning voltage 2 to correct voltage for c6 whilst playing a c6 from the sequencer
when you say you are struggling to set note 1 it makes me think you are trying to tune the pitches to each other - dont do that, do it individually to a reference. When both pitches sound correct on their own the curve should map them all.
Also check the oscillators of the target are set to default pitches and you have correct scaling type (one is linear the other isnt so will sound the wrong pitches).