It almost sounds like what I experience with my smaller size and FTP while riding with a friend who is heavier and 50+w higher FTP. I struggle to keep up on the flats, which is the raw FTP issue that exists between riders sometimes. Not sure if that kind of disparity can be felt on a tandem.
Could be kinda like that or maybe like the difference of pushing watts on flats vs hills?
How about cadence and such, are you both training at similar cadence and inertia otherwise (inside, outside, etc.)?