Thanks for the details. I couldn't find the cause, but I found a solution that simply excluded the search shortcode from the post processing.
Keep an eye on other 3rd party shortcodes as well. The search shortcode was altered by something, which added extra lines and tags between empty lines. This should not happen and may cause issues with other plugins that use shortcodes as a display method. If that ever happens, make sure to disable suspicious plugins one-by-one and keep refreshing the front-end until the problem is fixed. That way you will know which plugin might have caused the issue. If that's not helping, then most likely the theme is at fault.
I'm hoping it's not going to happen to other shortcodes 🙂
For future reference I changed, includes/shortcodes.php line 124:
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