Here is
part of the full Beads Stack.
Next
to the bottom Frame.
The
bottom Frame.
The
Picture after Do Stack
Finally Out
produced from the Picture above with Do Stack.
In this case the solution is simple, we want the Pixels in this rectangle to come from the bottom frame so we use Rectangle->Paste Active Over, having first made the bottom frame active with repeated Down Arrows or Control+Down Arrow. Remember to select a rectangle press the Left mouse button over one corner and drag a box around it.
You'l notice that as a highlight goes out of focus it forms a disk, the edges of the disk look like detail to the program and are picked up.
Here are some other suggestions that might help with this problem.
Remember you will probably want to Stack->Interpolated Output when you finish editing.