how are layers organized in gimp?

[Ofnuts]

As far as I can tell, this is because your bottom layer is transparent, and the layers above it are not in "Normal" mode (this is the "Mode" selector at the top of the layers list, unfortunately you screen shot don't show that value for the upper layers since you have the bottom layer selected). Compositing mode other than "Normal" usually keep the transparency of the bottom layer.