Drupal 6 site updates are not been applied I have a Drupal 6 site running fine, but when trying to apply updates to its modules by uploading the latest version of the module and visiting update.php the update process complete, but when I check the available updates report it still show me the old module versions marking them as outdate.

I can read and write in the DB, and I can upload files to the server so it is not a DB  or file permission.

Can you explain why the updates are not being applied/seen?
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?