I am having the same problem except that I have checked and the box for emptying the recycle bin is NOT checked.
I tested by deleting a small picture to the recycle bin and then restarting windows. When Windows is done starting everything I opened the recycle bin and the file is still there. I then immediately ran CCleaner v 5.61.7392 and checked the recycle bin and it is now empty.
I also put a check in the empty box for the recycle bin and closed CCleaner. I reopened it, unchecked the box, closed it and then opened it again and ran the program. to make sure there was not a phantom checkmark lurking in the registry. It still empties the bin.
Any suggestions would be appreciated.