If you have a "settings.php" file in your block's directory, the settings link will be available from the main "Plugins / Blocks" menu tree but will not show up on the main "Manage blocks" page. This is true unless there is a "has_config" function defined within the block that returns true. I believe this inconsistency is unintended.
One of two things should be true:
- Presence of the "settings.php" generated the setting link in both places, or
- Presence of the "has_config" function is required to generate the setting link in both places.