There is a bug with the Stamp Layers command. If you use cmd-opt-E (on Mac) with multiple layers selected, they will correctly create a new, merged layer at the top using the selected layers. However, if the only paint layer is the background layer, then the background layer will be replaced with the merged layers, and re-adjusted by the adjustment layers above it. There is no new layer created at the top. I believe this is not the intended behavior.