The number is supposed to be the amount you have in surplus / deficit every click.... like you rate of gain/loss.
It depends on what you are building at any given moment.
It's somewhat more complex than that, but that is the gist.
Does that answer your question?
If I understand the inquiry... you are asking why you might be gaining nodes, while your numbers are remaining in the negatives.
If you are building more things, or more expensive things, as you gain nodes, that would do it.
