My guess is the rocket wants to cone under lower thrust profiles and with harder hitting motors its probably more stable off the rail resulting in less "corkscrew" aka coning. An adapter plus 29mm motor may weigh more than a 38mm motor ( sometimes).
We need more data to make better guesses at the issue, things like motors used, rocket sim file, pictures of rocket, rocket weight and nose weight mass. Scale V2's are well known for "coning", "tail walking", "corkscrewing" due to relatively small fin area and the heavy noseweights necessary to make them stable, motor thrust profile can have a lot to do with how severe the coning is. Think trying to balance a sledgehammer vertically on your hand with the head being the nose, you have to use motion at the bottom to keep it balanced, its almost like coning, and the movement of air over the fins provides the corrective movement.