On July 30, 2016 I released an update to the Add Widget After Content in the WordPress Plugin Directory. The update fixes issues with the After Content Widget Area not showing or showing in the wrong position after the content. All you have to do is go to Appearance > Widget After Content in the WordPress Admin area and select the priority that works best for your site. For example if you use a recent post plugin you may need to set the priority to 10, so the widget area shows before your recent posts. If you use a page builder plugin like Beaver Builder set the priority to 99 so the widget area will show after the content added by Beaver Builder. I received messages thanking me for adding the new feature.
BUT then I started to receive emails, contact form requests for support, and support request from the forum that the update breaks shortcodes, adds random spacing, paragraphs, and breaks.
I was heart broken.
Then after responding to multiple requests that were all fixed by setting the priority in Appearance > Widget After Content, I realized why only some people were having the problem. Only people using a website manager such as Infinite WP and ManageWP were having issues with the format. If you update from the WordPress admin the default priority is set and all is well. If the default priority is not set it messes up the formatting especially for shortcodes.
I know you are asking well why does this happen?
It happens because Website Managers like Infinite WP don’t deactivate and activate plugins when they perform updates. So the default priority is not set during activation.
I messed up by not validating that the priority was set. I take full responsibility for my error. Another update will be out soon.
But until then …
It you have formatting issues after updating to Add Widget After Content go to Appearance > Widget After Content in the WordPress Admin area and select the priority that works best for your site.