Well, guess what? There might be a very simple solution to this problem.
Code:
ebook-convert eBook.epub eBook.mobi --margin-left=0 --margin-right=0 --margin-top=0 --margin-bottom=0
I cannot test this as the laptop only has Mobipocket Reader on it which doesn't have the K3 bug. Yes, the bug is not in the Mobipocket file but in the K3's renderer.