I'm going to "guess" it's not the penguin but a url issue. I've moved around 20 sites to a different platform and it's never been a totally seamless transition as far as google is concerned (none of them Drupal however). Also check your sitemap. (the url that google thinks it is). I think you may see a 404 error.
Not sure if this is relevant but you might check out this known issue:
Known Issues
- While Sub-pathauto works when drupal_get_normal_path() is called, if drupal_get_path_alias() is called, the hook to alter URLs is not invoked. Functionality that uses this function to compare things like page visibility settings will not match the sub-path processed URL. This is due to core bug #1248626: drupal_get_path_alias() does not invoke url alter hook while drupal_get_normal_path() does.
Good Luck . From one hyperfocuser to another