If the muffler's moving about, then aluminum particles will get into the exhaust and turn it black.

You can easily check by removing the muffler and holding a piece of white card stock behind the engine to collect the exhaust residue directly from the engine. You'll be able to easily see if you're still getting metal particles.

About the muffler. Don't get the long bolt too tight. You want it just tight enough to keep the muffler parts from moving. If the bolt's too tight, it will break when the muffler expands from the heat of running.