Knocking noise after new exhaust gaskets

I had felpro exhaust gaskets on my headers and they leaked bad. I put Remflex gaskets on and now it sounds like a random engine knock. It's not constant, only every few seconds and comes and goes. Can a exhaust leak cause this? Or is this a random failure in the engine?
Did you replace the collector gaskets? If you did, you probably turned the collector flanges and moved one of the piped close enough to something that the pipe is hitting it. I would check that first. You should be able to just loosen all three bolts and turn the flanges to reposition the pipe.