I bought this engine NIB with rc carb and silencer this last christmas and proceeded with break-in with no problems. I stored the engine some 2 weeks ago, after leaving it for 5 days outside the box so any corrosives would escape the crankcase, as for PAW instructions. Only today I removed it up to remove the silencer, the only intervention to it besides putting the carb needle on and off of it and adding fuel to the tank.
These engines have the head hold on to the crankcase by 3 screws, with the liner being exposed to the outside. The head has no influence on the portings. I also took great care when removing the head to take the silencer out so the liner wouldn't move from its position.
I'm really puzzled as to why the engine would not want to start with the silencer on since it has always started great from new. My other 09 C/L was started yesterday and it too took some fliiping to startup, but it had been stored for 2 months or so (it also hasn't got a silencer, one of the reasons why I bought the other PAW 09).