WordPress upgrade adding additional quote marks to shortcode output

This is probably the result of the wordpress 4.0.1 security fix which changed how shortcodes are handled http://wptavern.com/wordpress-4-0-1-exposes-bad-development-practices-used-in-some-plugins. While I am not sure about the details your shortcode handling seems to match the general description of trying to parse the shortcode by yourself instead of properly registering it.

To fix this you need to create, register and handle an “item” shortcode.