Same thing occurred for me after activating the plugin.
I got round it by changing the entry in my wp-config.php file. The line read:
define( 'AUTOMATIC_UPDATER_DISABLED', true );
And changed it to:
define( 'AUTOMATIC_UPDATER_DISABLED', false );
I think this is how it should be…
I have solved the problem!
The culprit was the ABP AdBlock Plus Firefox plugin. To solve this issue – click the option drop-down on the ABP icon (in the browser window) and make sure that you have disabled it on the site you are working on – kind of obvious I know but I did not expect it to disable the actual available widgets in the WP dashboard.
Disabling the ABP will re-instate your Header and Footer widgets 🙂