This could easily be related to the crop choice you made when placing. If you chose art or bounding box, there's a good chance that the the size of that box changed after editing.
It could also be the preference setting under File Handling for links. Make sure you have Preserve Image Dimensions When Relinking checked.
My settings are correct in the file handling....and it's not the box resizing - it's the artwork inside. What setting should I be using in the place options>"Crop to" box?
Either "media" or "crop" should be a choice that does not change when you edit the art in Illustrator, but both of those are going to give you more white space around the are in the frame, requiring you to manually scale and crop inside ID.
thank you! I will give that a shot.....