Haven't so far done it on Windows 7 but I always set the Registry in XP to keep only the files needed for booting. Below is the fix.
Altering Prefetch Parameters
Prefetch is one of the commonly overlooked components that can have a significant impact on system boot time. This tweak allows selection of which components will make use of the prefetch parameters. To see which files are gathered using each of the settings, clear the prefetch cache located at C:\Windows\Prefetch and then enable one of the settings. Clear the cache and repeat for each setting.
[Start] [Run] [Regedit]
Registry Key: HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager\Memory Management\PrefetchParameters
Modify/Create the Value Data Type(s) and Value Name(s) as detailed below.
Data Type: DWORD Value // Value Name: EnablePrefetcher
Setting for Value Data: [0 = Disabled / 1 = Application Launch Prefetch / 2 = Boot Prefetch / 3 = Prefetch All]
Exit Registry and Reboot
Please check in the Registry if the setting for Value Data is 3
PS: Some cleaners have a setting to automatically delete all Prefetch Data. I had it in a cleaner named SuperCleaner that I was once using. I have never used CClleaner but there may be a similar setting there too.
And finally there is hardly any real harm done if the prefetch data is getting deleted. You can switch off the error message in Tuneup Utilities if you so desire.