In the "Publishing" section of the "Edit Layer" page, the Default Style legend is always the generated one.
If the selected style specifies a custom legend graphic, it is not displayed in the page.
This does not affect the "GetLegendGraphic" wms requests, only the administration interface.
To reproduce with the standalone package:
Edit the "rain" style to add "grass_fill.png" as custom legend
Verify is works correctly via WMS: http://localhost:8080/geoserver/nurc/wms?service=WMS&version=1.1.0&request=GetLegendGraphic&layer=nurc%3AArc_Sample&format=image/png
Go to the nurc:Arc_Sample Edit Layer page and select the "Publishing" tab
Under WMS Settings --> Layer Settings, the default layer is "rain" but the legend is the old one.