@Ivan: I guess you can achieve the same behavior as in photoshop by locking all the layers except the one you need. we would like to keep animatron as simple as possible, so new checkboxes will be introduced only when absolutely necessary.
@Liga: I am sorry I still don't understand how you do it. I tried selecting layers in layer area and changing their order or position on screen etc, works fine. I also tried selecting objects on the canvas and doing all kinds of manipulations, fine as well. Does it happen all the time or just occasionally? Can you share the project with us?