I take it you mean it clones from all layers, rather than just from the layer you selected your source point from? It is rather annoying. There needs to be a checkbox to clone from source point layer only or all layers.
Just as an aside, as you know, Photo-Paint, by default, clones in a similar manner to having the Aligned checkbox ticked in Photoshop. To have your clone keep reverting back to the souerce point (where you right-clicked) as it works in Photoshop with the Aligned checkbox unticked, hold down Alt+Shift (make sure you press Alt first!) and then right-click and clone. As long as Alt+Shift is continued to be held down, you can release the mouse button, move to another area of the image and start cloning again. Cloning will commence from the original source point again.
I don' think I worded that very well lol.