Drupal 6 site updates are not been applied
Did you clear the cache? 

Are you sure you are updating the right modules? Drush for example will place modules in sites/all/modules, but if your modules are placed in profiles/profile/modules Drupal might still be reading the old modules.
Drupal won't complain if you are having duplicates, only on enabling.

Can you confirm the modules are read? Check the database, are the module path correct? Is the info file of you modules showing the correct version?