Shutting down the iMac with El Capitan

Recently, when I try to restart or shut down my iMac, all icons on the desktop would immediately disappear as if the computer is about to do that but it never restart/shutdown.

Also, after awhile if I decide to open apps or documents, they will open normally, which means the restart/shutdown process doesn't seem like it's going on.

I have tried different things suggested online such as verify disk, reset PRAM, etc. and none of them seem to help.

The only thing that seem to work is by using a Terminal but I am afraid I might damage the computer if I continue to rely on that method.

Is there any other way of fixing this?