Whenever you switch your site to a new CMS (joomla, wordpress, pligg, drupal, whatever) you have to be very careful. There are countless potential pitfalls and unfortunately it sounds like you fell into at least one pitfall. Here are the most common pitfalls: 1)rewrites robots.txt to block search engines from all pages 2)add metatags to each page to block search engines 3)add metatags with improper language/location info that limit you to country specific serps 4)break your old link structure 5)rewrite all url addresses
If I were you I would check out the robots.txt, the metatags on your pages and make sure you do not have any 404 errors. If you have any 404 errors you should use a 301 redirect to send them to the new page and if you dont have a new page then create one asap. Good luck.