Create a new notebook with the following two input cells:
NotebookWrite[EvaluationNotebook, Cell[BoxData[ToBoxes[Manipulator[Dynamic[x]]]], "Output"]]
y = 10 (* dummy cell *)
If you evaluate the whole notebook (
Evaluation menu\Evaluate Notebook), you will see the manipulator appear then quickly disappear.
If you manually evaluate the first cell, the manipulator will not disappear.
Why is this happening?