My life would suck without you
Okay so if it is in fact the berry glitch and not the internal battery running dry, you can fix it by connection the game with any Gamecube game or by pressing B, start and select on the FR/LG/E menu screen, and by following the prompts.
The white rock is just a decoration. Fun to speculate about it though.
Also if you need berries for a Milotic, wild Spinda, Whismur and Loudred can have a Chesto Berry as a wild hold item.