Let's take another look at the basic principle that determines which programs show up in the Start menu:
Each time you launch a program, it "earns a point", and the longer you don't launch a program, the more points it loses.
If you stare at this long enough, you might see a hole in this principle: What about a program that you launch once and keep running all the time? According to the rule, this program would "earn a point" when you first launched it, and then it would gradually lose points⊜ even though you clearly use this program frequently. (Here, "frequently" is an understatement for "all the stinking time!")
Thus was born another fine-tuning rule: For each consecutive day◊ a program was kept continuously running, it "earned a point" as if you had launched it yourself.
This little "feeding the program points under the table" was enough background radiation to keep the program afloat in the points race, but not so much as to overwhelm the programs that you actually launch frequently. After all, if you keep the program running all the time, the Start menu didn't have to give the program high placement. Most of the times you open the Start menu, you don't need to launch that program; it's already running. The program just needed to be kept from dying out completely.
⊜In extreme cases, it might even drop all the way to zero, at which point the program would act like you'd never run it at all!
◊"Day" here is shorthand for a more complicated definition (taking into account idle time), the details of which are not relevant.