Loralyn, I’m not here to make any money off my fellow Veggies 😉
I think I’m misunderstanding the screen captures you posted… I don’t see any reference to the Track Motion part of the issue, unless its position at 0:00 is where it should be for all instances (?)
Just to rule out more “duh” thinking, I don’t know if this is contributing to it, but if I were in your shoes I would adjust the crop first on the raw clip, then go on the project timeline to where the picture-in-picture needs to be and use Track Motion to position it. That will introduce a keyframe at that place in the timeline. Then, I would copy that keyframe, go to 0:00 and paste it there as well, so that both positions have the same position coordinates. And, make they keyframe type “Hold” for both. Or, you can simply make both positions “Holds” as well (instead of copy/pasting one to the other).