The muffler retains a lot of heat in the engine, which isn't so good for new motors.  It also changes the sound, sometimes making it difficult to figure out if the motor is too rich or too lean.  That said, I ran the Brodak 40's with the muffler right from the start with no problems.

Hi Peter,
As Phil C did, I ran my B.40 with the muffler from the very start, with absolutely no ill effects. In fact, that is one excellent B.40; flawless running characteristics, easy cold start; "twitchy" hot-start (very easy to flood when hot), very good power. I took great care not to let the engine overheat, using the "thumb test" on the cylinder, and a Great Planes Infrared Thermometer on the crankcase frequently. Break-in was a long series of 1-minute runs at a "rich 2-cycle", followed by a complete (5-minute) cool down, with gradual leaning and lengthening of the run cycle.

The nearest place where I know I can run unmuffled is 40 miles away (Scobee Field) and that's just too !@#%$ far to go to break in an engine! I'm about to break in several other engines, also without the 80-mile round trip, as soon as I get the new test stand completed.

Oh yeah. Always do break-in with the same fuel you intend to run in the plane, and with the maximum nitro content you expect to run. The engine actually runs cooler (at the same power setting) with nitro than without! Take your time!

EDIT: Spelling, naturally!