placed, linked images shift position when link is updated...

Hi there. I place package comps created in AI in a PS image of the store shelves. I'm having an issue with my placed, linked AI files shifting. It happens even before the linked files are updated, actually, but it does the same thing after the linked files are updated. (The mask is applied because sometimes there is more than one package on the AI artboard.)

Here's what happens: When I resize a placed and linked AI file that has a layer mask, the layer doesn't line up with the mask after it's resized. I've tried a couple of different crops when importing. The Bounding Box crop is more predictable than the Media Box... but the bottom line is that regardless of which crop I use, when I update the linked doc and go back into PS, I have to unlink the masks and manually reposition the layers to get everything to align. I am sure this is not an efficient way to use this feature...  and that I'm not ticking or clicking the right boxes here. Being an InDe user doesn't help, because obviously PS behaves differently. What am I missing? 

I've attached a couple screen shots that might help explain... 

And if there's a better way to do this, please point me to the tutorial! We are constantly iterating concepts in one way or another, and then have to pull them into a presentation doc to share with the clients. The package designs are shown in the presentation by themselves and on-shelf, so the idea is to use only one doc to make the designs and then place the one doc into both the presentation file and the shelf image PS file so that the changes get updated in both places. (personally I would do the presentation in InDe, but this is the process we are supposed to follow... )