Items in desktop folder to appear on desktop
Solution 1:
There is an option in path finder to hide finder's desktop and replace it with a version provided by path finder.
You might want to try reinstalling it and checking its preferences, particularly the general preferences section.
Solution 2:
If you don't want to reinstall PathFinder, you can type this command in Terminal.app
defaults write com.apple.finder CreateDesktop -bool true
This will get them back. You might have to log in and out.