At the moment you can’t fill unused parts of the deathnote with Black. I have to get around it by first filling it with any other color, and THEN filling it with black.
I was writing the same bug report 
What happened?
The Fill-tool did not fill a blank area with black.
What was SUPPOSED to happen?
The blank area on the DN would have been black.
Steps To Reproduce:
- Use black ink
- Use fill tool
- Watch as you never get the ink on it, and even manage to confuse the system if you spam.
Comments:
You can avoid the bug by using the fill tool to first with another color, then Black.