As the thread title says, I'm disabling whispers in the settings and as soon as I hit save, the checkbox is still checked and whispers are still active. I've checked the config file and it is set to 0.
I suppose something after the config file could turn the setting back on... Try turning all your extensions off, then see if the checkbox clears. If it does, turn on extensions one at a time until it comes back on. Then you have found the cause.