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.
Ken, Cool find. Note that the history step that is recorded is "Stamp Layers" not "Stamp Visible." Try using Cmd + Opt + Shift + E as your workaround. You'll not in this case, "Stamp Visible" is performed correctly. We'll take a look at this. One of the problems with changing something like this that it may break existing actions that expect the current behavior (Even if the present behavior is somewhat expected) - so that may affect our decision making on performing a change here.