I've just seen this and it seems you still haven't solved the issue. I bet you have updated the metadata.json file and then replaced the file with a new Q2A release so the changes got lost. In order not to rely on having to modify core files you can just do what Q2A does in order to remember the enabled plugins.
1. Enable all the plugins you want to have enabled
2. Run this query against the database:
SELECT content FROM ^options WHERE title = 'enabled_plugins';
The output should look like this (note the xml-sitemap plugin will be there):
basic-adsense;event-logger;example-page;facebook-login;mouseover-layer;opensearch-support;recaptcha-captcha;tag-cloud-widget;wysiwyg-editor;xml-sitemap
3. Configure that string to be applied to the enabled_plugins key of the options table after initialization. For example, you could do something like this:
qa_opt('enabled_plugins', 'basic-adsense;event-logger;example-page;facebook-login;mouseover-layer;opensearch-support;recaptcha-captcha;tag-cloud-widget;wysiwyg-editor;xml-sitemap');
If this works after the first refresh or after the second will depend on how you reset your site.