I would recommend downloading Process Explorer from sys internals and check for process using large amounts of CPU/memory/Disk activity.
Process Explorer
Also I would suggest you check the event log for any errors. May give you some indication of a problem.
Start,Run, open 'eventvwr.msc' Then check the system log under Windows Logs
Another place to check is Control Panel > Performance Information and Tools > Advanced Tools
Try the top and bottom options
View Performance details in the Event Log & Generate a system health report.
Hopefully that gives you some leads.