Ok, I have found the culprit.
defaults write com.apple.finder DisableAllAnimations -bool true
defaults write com.apple.finder AnimateWindowZoom -bool false
After some testing I've found the setting which caused that:
I disable additional Finder animations with that tweak (it is a secret Finder setting). Unfortunately it is not that well tested probably and it introduces this ghosting (probably because Finder's icon removal code is not called when animations are disabled).
You may try to enable the animations again and reset Finder (CMD+OPT+ESC) and relaunch TotalFinder again. But I'm afraid you will get some visual glitches with TotalFinder.
Solution:
DisableAllAnimations must be false and AnimateWindowZoom must be true, also we have to disable TotalFinders internal override of these tweaks.
Please execute this as single line: