The first subtlety of the basic principle that determines which programs show up in the Start menu is something you may not have noticed when I stated it:
Each time you launch a program, it "earns a point", and the longer you don't launch a program, the more points it loses.
Notice that the rule talks about programs, not shortcuts.
The "points" for a program are tallied from all the shortcuts that exist on the All Programs section of the Start menu. Many programs install multiple shortcuts, say one to the root of the All Programs menu and another to a deep folder. It doesn't matter how many shortcuts you have; if they all point to the same program, then it is that program that earns the points when you use any of the shortcuts.
One the Start menu decides that a program has earned enough points to make it to the front page, it then has to choose which shortcut to use to represent that program. This is an easy decision if there's only one shortcut. If there are multiple shortcuts to the same program, then the most-frequently-used shortcut is selected as the one to appear on the front page of the Start menu.
If you paid really close attention, you may have noticed a subtlety to this subtlety. We'll take that up next time.
Please hold off your questions until the (two-week!) series is complete, because I suspect a later entry will answer them. (This series is an expansion upon the TechNet column on the same topic. If you've read the TechNet article, then a lot of this series will be review.)*
*I wrote this last time, but that didn't stop people from asking questions anyway. I don't expect it'll work today either, but who knows, maybe you'll surprise me.