Certain "special" Pokemon cannot be traded over the GTS. "Special" meaning event. If you try and trade an event Pokemon to someone who isn't on your friend list, it will tell you that because of the Pokemon being Special it cannot be traded. Manaphy is an event legendary, and so cannot be offered for trade on the GTS. That is why the search fails.
And yes, the game will still recognize the Pokemon searched if you type in all caps.