It's to prevent double spend attacks and delay arbitrage between exchanges.
You may not like 999 confirmations but it does prevent the price from tanking every time there is an attack. This is better for the coin in the long run.

Also this wouldn't even be an issue of they just changed the mining algo.. As long as the coin is using Scrypt is vulnerable to attacks from large mining operations. (this is something I advised them to do years ago but nobody took it seriously)

There is always a huge run up before a new wallet update and then dumping happens afterwards when people realize that the wallet update is not the magic bullet that will take them to the moon.

People are mad to buy at high prices expecting it to go even higher, there is always a correction after a huge jump in price.