What you are describing is an ability to play good poker with normal stacks (such as NL cash games), while struggling when the tournament enters the "endgame" stage. In MTT's with fields of 2000+ players, the endgame stage actually takes up a majority of the tournament. Basically anything beyond the first ~2 hours of play will fall under some varying degree of endgame.
If you haven't already, you undoubtebly MUST obtain a copy of HOH2...
http://www.amazon.com/Harrington-Expert-...7310&sr=8-2
This covers all the concepts you've asked. Once you've done so, things will start becoming more clear, and you'll slowly recognize different situations that you never did before.
Also, HOH1 is a very worthwhile read if you haven't already. It just doesn't cover what you're asking here.