After upgrading a site from CiviCRM 1.9 to 2.0.1, a custom group had disappeared from the contact record's interface (view/edit). I compared the civicrm_custom_group entries with those who were being displayed, and found that changing the value of the fields "civicrm_custom_group.extends_entity_column_name" and "civicrm_custom_group.extends_entity_column_value" to NULL (instead of an empty string) fixed the problem.
16:08 < bgm> in CRM/Core/BAO/CustomGroup.php, I see places where it explicitly checks for NULL
16:09 < bgm> around line 191
16:09 < bgm> the field extends_entity_column_name doesn't seem to be used at the moment (2.0.1)
16:36 < dlobo> bgm: will check and clean for 2.1
16:36 < dlobo> wanna file an issue