up down gear recording on float planes.

 I land on a runway with a gear down warning, fine. Taxi into the water, raise the gear and take off and still have the gear down for runway landing warning even through the gear is clearly retracted? Should get a gear retracted for water landing. Also can land in the water, come to a stop, lower the gear to  pull up on the beach and not get the gear down for runway warning. Yes the gear indicator lights are working correctly. It only counts the runway landings in the logbook. Now I am really confused. Same on all aircraft as far as I can tell.