What were the timestamps for navigation.position? Timestamps are critical here. Signal K may display positions even if they aren’t being refreshed, but Saillogger will only use positions if they are actively refreshed. When you encounter an issue like this, please verify those timestamps.
Generally, there’s no technical reason why a GPS position in Signal K wouldn’t appear in Saillogger. Saillogger retrieves data directly from Signal K, so as long as the position is present and refreshing (refreshing is essential), it should definitely capture it.