the rule of thumb is using the domain version that you have registered in webmasters tools.
>>>> You meant in google's webmaster's tool website or from your extension?

If you had previously entered some metainfo for links without 'www' they won't be showed anymore for links with 'www' because links are changed and different so this is normal. But you should be able to work with analyzer and seo spider as well as before this is not normal, evenutally try to clear all the Joomla cache that's could be the problem and ensure that sitemaps are not cached. If you have issues just revert to the previous domain.
>>>> My joomla already cleared (was nothing in it) and sitemap not cached, precache was off.

So you are saying setting it to either one www. or without wont hurt the other when indexed by google?

Thanks,
Teddy