I have the same problem. Using Classic Icons, there is a black box or square partially or totally over your icons. It does go away if you make them bigger, by Control+Scrolling Mouse Wheel or selecting Medium instead of Classic icons. Deleting the icon cache and rebooting several times hasn't helped. In fact, formatting and doing a restore back to out of the box. I can't find my bookmark but seems to me that years ago it was solved by someone saying to go somewhere and do something that resulted in the default size of icons (where they are stored, I guess) is changed to a lower pixel number.
Yes, my resolution is reduced as I have poor eyesight.