Just a guess, do you have any maintenance application/utility set to run on schedule like CCleaner or some others...?
Most can also be set to clean on startup.
Those have the ability to automaticaly suppress old prefetch data. Normaly, "old" is something like over 14 days to 1 or 2 months. That threshold can be changed to any value down to a single day.
Check the settings of any such utility. If needed, set them to a much less agressive level.
Electro, August 2013