The taxonomy module was updated with Drupal core version 6.24.

Line 730 of taxonomy.module (Drupal version 6.24):
$node->taxonomy = taxonomy_node_get_terms($node, 'tid', TRUE);

...leads to the loss of tags, which have been submitted by the author of an article during it's creation.
"My tags" can be still be applied.

Deleting Line 730 mentioned above solves this issue, but since modules should adapt to the Drupal core and not conversely, this should be fixed in the community tags module.