I am not too much getting , how the selection of cells works here : I press "i" after moving the cursor to the substrate via cell , but this is selecting the TOP level layout fully , not the cell itself - What could be the reason ?

It doesn't work if you have the cursor directly over the device gate?

I was not clicking over the gate i think. I was clicking over S/D areas.

That shouldn't matter, though. How about the "select cell" command?

right now , clicking the gate and pressing "i" multiple times seems to help THans

The fact that you have to "click" makes me wonder if the issue has to do with the focus policy in the window manager. I use a focus-on-enter policy so that as soon as the mouse is in the layout window, it has keyboard focus, and keystrokes are interpreted as macro commands. What you describe sounds like behavior you might get from a click-to-focus policy.