I have long encouraged customers to do regular maintenance on their systems so solve problems such as this.
Right-click on the C drive or other drive you want to do maintenance on and go to Properties. If your Disk Properties window has a Tools tab, sellect it. Preform the Error-checking and Defragmentation functions on the drive.
This should help restore some of quickness in the boot time of your system. If it's still a problem, consider leaving the system on.
