|There must only be one " Prefetch " folder in Windows directory. There cannot be more than one folder with the same name. Check if one of the folders has a blank character in its name. Delete the one with lower-case letter p. Also delete everything in the other Prefetch folder and reboot. Windows will re-create the files in Prefetch folder as you start using your programs.|
Also check if Superfetch service is disabled. It should always be on Automatic.
To answer your question " ...If it is looking for something in there which is not there,
how comes deleting everything helps? "
The answer is, there may be a configuration data in Prefetch folder that belonged to a program that you had some time ago but that program no longer exists. Windows may be looking for files, .exes, .dlls, etc. of the now non-existent program according to the Prefetch config data.
This may not be a solution to your issue, but you lose nothing trying.