So your saying if you load a hd with "stuff" (being very un-spedific on purpose) it will slow down the speed at which it opens a program? I would agree if you put installed programs as the stuff on the drive.. but if you a hd 90% full with music, or movies (legal ones of coarse) It would not affect the speed the program opens. What you need to keep in mind when you install a program it also installs dll's and other things your computer will be running along side that opening program you will be speed testing. If your gonna load the hd, do it with data, not an installed program.
Also your worried about the time down to hundredths of a second, you should look into some other factors which will hinder the accuracy of the data. Those being... How long the computer has been on, the ambient temperature of the inside of the pc, and of the room. *if any other programs have been installed* Anyway hope that helps...
My hypothesis: The hd seek time on a loaded hard drive (data) compared to an empty hard drive will not effect the speed of the load to any *noticable* or significant amount.
Have fun