Created attachment 104155 [details]
Kra file already set up and consistently bugging on my machine.

!! BEFORE YOU TEST THE SAMPLE FILE !!
You need to resize the image as I shrunk it down to attach it here. The real hight is 4960px and consequently the width is 3508px.
!! THEN YOU CAN GO ON !!

When using the magic wand and clicking to select, sometimes nothing happens with "big" files like A3 300dpi :

So here I am, with my proud Frame layer delimiting my panels. 
I click inside each hole (limit selection to current layer) and transform the selection into transparency masks for each panel (which are group layers) to make sure my strokes don't overlap between panels (the thickness of the frame is not enough to cover my strokes).

I realized recently the magic wand was working kind of randomly. Sometimes I use the wand and it's fine sometimes not. So I took my actual file where it is consistently bugging and marked down where it works and where it doesn't:

I can only select the first hole I checked in green in my attachment sample kra file. The others won't work (unless I resize down the file so it can be attached).