I have noticed on a few occasions that when upgrading from Drupal 6 to Drupal 7 when running update.php things seem to go alright with the first update.php. However, if you execute update.php again you'll have update items that did not complete and will not complete until you fix the code. In particular there are some db_insert() queries that will fail due to duplicate entries for the data being inserted. I have found these in both modules/system/system.install and modules/block/block.install. The simplest resolution to these is to modify those files and wrap the insert with a try {} catch() {} block similar to shown in the api documentation[1] except when you catch the event you need to continue on.
[1] http://api.drupal.org/api/drupal/includes%21database%21database.inc/group/da...