Open ~/.conkyrc and see if this section reads the same as mine.
# Create own window instead of using desktop (required in nautilus)
own_window yes
own_window_type normal
own_window_transparent yes
own_window_hints undecorated,below,sticky,skip_taskbar,skip_pager
If it doesn't read the same then change it so it does.
Back up the old file first.
Fujitsu Lifebook AH532 Laptop. Intel i5 processor, 6Gb ram, Intel HD3000 graphics, Intel Audio/wifi. Realtek RTL8111/8168B Ethernet.Ubuntu12.10 (Unity), Mint14 (Cinnamon), Manjaro (Xfce).
