One time I had a similar situation. I found by rebooting 2x I can restore my system permance back to what it was. Use the system for 20 minutes. This will give a chance for delayed startup items to finish loading and complete the background tasks (when idle) such as the search indexer.
If readyboost no longer seems to be working then try disabling readyboost on your flash drive then re-enable it. Under Computer, right click your flash drive and select properties. Goto the readyboost tab and select "Do not use this device". Click Apply. Then re-enable readyboost and click apply one more time.
Moving on. I dont use the "Old prefetch data". Instead, I have several items in the Include for cleaning useless pf files.
CODE
Include1=PATH|C:\Windows\Prefetch\|_*.pf
Include2=PATH|C:\Windows\Prefetch\|dllhost.exe-*.pf
Include3=PATH|C:\Windows\Prefetch\|autorun.exe-*.pf
Include4=PATH|C:\Windows\Prefetch\|MSI*.pf
Include5=PATH|C:\Windows\Prefetch\|!*.pf
Include6=FILE|C:\Windows\Prefetch\|*demo*.pf
Include7=FILE|C:\Windows\Prefetch\|install*.pf
Include8=PATH|C:\Windows\Prefetch\|RUNDLL32*.pf
Include9=PATH|C:\Windows\Prefetch\|*setup*.pf
Include10=FILE|C:\Windows\Prefetch\|*tmp*.pf
Include11=PATH|C:\Windows\Prefetch\|unin*.pf
Include12=PATH|C:\Windows\Prefetch\|*update*.pf
Hope some of that helps. In a short time you'll get your performance back. A good drive defrag always helps things along too.