KOReader does not replace anything on the Kindle, it's just a 3rd party program running on top of the normal Kindle OS. KOReader screen savers are part of KOReader, not any part of the Kindle OS. If KOReader is not running (ie. you are in the regular Kindle UI) then obviously the KOReader screen savers can't be shown.
There are other projects to modify the actual Kindle screen savers but chasing after it via KOReader is a wild goose chase.
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