I have v2.19.901 running on Windows XP. While CCleaner always cleaned 100% in the years I've had this program, for the last couple of months it only cleans 98%, even if I run it again. It is as if there is a "protected" program running in the background that I can't touch. I would welcome any suggestions on how I might bring the cleaner back up to speed.
Try running CCleaner in Windows Safe Mode. And if you're using Windows Vista run CCleaner with administrator privileges which you can do by right clicking it's desktop icon.