This may be because the new markup did not override the one from WordPress yet. More information can be found here. If that is not your situation, another reason may be because of plugin conflicts. For example, your Performance plugin might have a section to minify the Javascript. The algorithm selected will remove the schema markup when it shouldn’t. You will need to change the settings of that plugin to not remove our Javascript. If you need help identifying this, please contact support@schemaapp.com.