issue with the transform tool which transforms 2 objects differently

It's been a long time i have this issue and this far I always found a hack to go around the issue, but i'm sick of it as it's a basic tool that I used for years and i don't understand this strange behaviour.

I joined a file to explain what I do ;

It's very simple, I have two smart objects one above one over ; I want to resize both of them. 

The overview is good, so I press enter, and BOOM! Everything explodes.

I'm sick of it lol...

I tried adding a .txt file in the preferences folder with "TransformProportionalScale 0" inside ;

I tried changing the preferences (inherited transform)... (see caption also)

don't hesitate to ask me further questions...