There could be several reasons for your problems but one thing you should look at (especially after this latest update) is “compatibility mode”. Since other plugins could use similar shortcodes syntax (ex: [button]) which could break the code, the plugin authors may give you a check box for “compatibility mode” where they will prefix the shortcode (ex: [su_button] or [gn_button]) to avoid conflict.
This latest version (4.5.0) includes a new “Shortcodes prefix” textbox under the admin menu “Shortcodes->Settings” where you can specify the prefix you want to use. Put in the value you are currently using (include the underscore) and click the “Save changes” button. Be sure to read the warning for using this feature!
