Most of the combat encrypted messages are sent to the Captains log and may or may not be sent as a "Radio" message. If you want the message in the Ships journal, you need to decode the message first and then transfer the message to the Ships Journal via the note pad (Schlüsselzettel).
Quote:
You can click on the Bedeutung Blatt white space and start typing
the meaning of the transcribed message groups. Then click on
the bottom icon to send the message to the ship log if you want
to keep it.
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Make sure you exit the game via the main UI. If you exit straight to Windows, the current entries in the Ship's Journal will not be updated.