Prefetched files will start improving your comps performance in about 1 or 2 weeks... Some recommend that you delete the prefetch folder once in a while (especially if you add/remove programs frequently)... Unless you have DISABLED prefetching (which, from what you indicate, you havent), you dont have a thing to worry about... Just keep using the programs regularly and in a short while, things should be back to normal...
Arun