I have heard of instances of certain cold air intakes that, in the name of increased air flow, make the MAF housing larger than stock, which will result in leaner running (because the MAF is not reading correctly, anymore). I'm pretty sure that the K&N Typhoon is one of those with this particular problem. I don't know that it necessarily causes CEL, and obviously doesn't for everyone, but Walter Marcy of Marcy Motorsports is one of the people who pointed this out, I believe specifically for the K&N Typhoon.
As far as I know, if you have a cold air intake that has a larger than stock MAF housing, there's nothing you can do about it except: (1) live with it and risk damage to your engine if it really is experiencing knocking (seems odd it would be that bad, and I would think the knock sensor would reduce timing to eliminate spark knock, reducing power); (2) buy a different cold air intake (I know that my F2 intake has a stock-size MAF housing); (3) get your car retuned for the difference in MAF housing size; or (4) put your stock intake back on.