Layers are unique and independent, almost all tools and effects can only read and write in the current layer.
I can't view your screen captures from here, but:
> when i create a new layer, then grab it, it draws a black square that covers the object
It sounds like you used the right mouse button to grab. It replaces the grabbed part by pixels of your current BG color. If this BG color is the same number as your image's transparent color, it really erases (becomes transparent, you see other layers below). But if it's a different color, it draws solid pixels in its place. It can be confusing if the image's transparent color is "black", and you also paint in "black" with an other color index.
> but does not select it and also grabs the object from layer1.
The brush-grabbing sees only one layer, so if you don't capture the brush that you expected, it means you grabbed from the wrong layer, or you had drawn the shape in the wrong layer.
Note that when you right-click the button of the currently active layer, it hides all others (or shows them back). It's very handy to check the content of a layer.
Here's a test image, it can help experiment with the tools:
http://grafx2.googlecode.com/issues/attachment?aid=6958252391428804566&name=12345678.gif&token=8b83c394aa744636d6150b1e670e153f(Attachment from page
http://code.google.com/p/grafx2/issues/detail?id=7#c26 , use button "download" because button "view" fetches a flat PNG copy.)
The "1" is written in layer 1, "2" in layer 2 etc. All the rest is transparent.
