It seems such a fundamental issue!
Ive taken to assigning students "0" when they complete the work so that any students who havent submitted their work show as a "-"
I have considered hacking some code, but I avoid working with custom code to ensure that we can quickly move to new versions - plus I may not always be at this school and i dont want to force any new person to have to maintain code.
Please keep me posted - i will let you know if we resolve anything. I may copy the gradebook module and add some tweaking so that we can always use the old gradebook in new versions.