The dealer tech is full of crap. The chip may have thrown the tune off enough to cause a knock, but I doubt it. And he's really full of $h!t about the filter. They love to use aftermarket mods as a scapegoat, either because they can't find the problem, or are too lazy and just want to stop once they see the mods, looking for an easy way out.
I'd go to another shop and get a second opinion. Also, post this problem on the main board. You'll get a multitude of responses similar to mine with regard to dealers and aftermarket parts. You might even get some troubleshooting ideas from the experiences of other members here.