We can imagine all sorts of possible and impossible scenarios, but the only way to know for sure is to put the bike on a repair stand and watch the chain very closely as it's put through its shifts and just about to jump off the offending cog. That said, since I can't see the bike, here's my suggestion for a possible scenario that hasn't been suggested yet. While in the big ring the cage hangs vertically or somewhat forward of the axle, but from the small ring it hangs rearward to vertical. If there's a slight twist in the hanger, that will change the angle of the chain as it tries to mesh with the cassette cog. When aligning a derailleur hanger, check for longitudinal as well as vertical alignment.