I just did a test and it's working for me. That is what I did:
- Created a new subfolder called "test" inside the images subfolder (not the one inside publish!!)
- Put there my test.png image.
- Added projectFolder/images/test/test.png to the assets. I can see the subfolder in the Library > Assets panel.
- Dragged and dropped the image in the stage.
- Saved the project
- Published the project
- The image test.png is always inside its subfolder.