Hi Andrei,
That looks like a correct command line to me and my attempt to recreate it seem to work for me.
Can you try quoting the 10,10 and see if works, I'm worried that somehow the shell is interpreting the 10,10 incorrectly.
C:\Program Files\Allegorithmic\Substance BatchTools 5> .\sbsbaker.exe ambient-occlusion-from-mesh --output-size "10,10" "C:\Users\Merle Boule\Desktop\ATKit\test.FBX" --output-path "C:\Users\Merle Boule\Desktop\ATKit"
David