Over the years I have often answered questions from players who just got a new instrument and are having trouble with intonation. This is especially likely when the old horn was a non-compensating instrument and the new one is compensating. The intonation tendencies can be different (or even opposite) between the two types. A major issue here is habit, which is very handy for some things (like when you practice scales so much that your mind/body system plays almost automatically after a point), ...