Not possible to give any definitive answer with the information provided. I know not getting an expected result is annoying but there will be something in your workflow causing the problem.
If possible post the Gimp xcf file with all the layers
or
A full screenshot showing the layers and tool options docks might provide a clue.
If you still have the Gimp .xcf with all the layers intact, it is always better to use Layer -> New from Visible rather than merging layers.
If possible post the Gimp xcf file with all the layers
or
A full screenshot showing the layers and tool options docks might provide a clue.
If you still have the Gimp .xcf with all the layers intact, it is always better to use Layer -> New from Visible rather than merging layers.