Should I be concerned?  I ride my S40 to/from work, about 11 miles each way.  I usually get home around 5:30 and I have noticed that the transmission casing on my bike is still too hot to touch as long as 2 hour later.  It seems to take a full 4-5 hours before the noticeable warmth goes away.  Is it normal for it to take so long for an engine to cool down after a 20 minute ride?  Engine oil level is good - about halfway between the Low and Full marks.  The exhaust seems to cool down very quickly and does not stay hot like the transmission part of the engine.  The bike seems to be running fine otherwise, although I am still in the break-in period (340 miles as of yesterday).  Any input would be greatly appreciated.

When I return from a ride on any of my bikes I always leave them to cool somewhat outside in the drive in the shade where the air can circulate. I have a neighbour who rides into the driveway, opens the garage door, puts the bike in a hot garage, closes the door and leaves it to bake.  

sounds normal.  I used an infrared thermometr before on an old Gravely lawn tractor.  I could not believe some of the temps I was getting.  The exhaust manifold was in the 900 degree range!  
My point is that the engine gets up to operating temp and can stay there indefinitely so it shouldnt be a problem even in a garage.

Thanks everybody.  You have convinced me that it is perfectly normal.  In fact I am so convinced that I just took a nice Saturday morning back country road ride.  

I've heard this, but I cant figure from whence does the heat come that increases the engine temp after shut off. Seems to me that if I extinguish the fire that is creating said heat, it should only get cooler.Anyone help me unnerstand this, or is it urban legend>?

The phenomenon is known as "heat soak." The engine generates heat internally as it runs. That heat moves from the combustion chamber (including the piston crown) through the metal to the coolant, whether that coolant be liquid or air. When the engine shuts down the coolant flow usually stops. Residual heat continues to flow out of the engine, but the coolant is no longer removing it. The result is that the engine usually heats up a little, then begins to cool by normal air circulation around it. On liquid cooled engines the coolant can still circulate by convection. On those liquid-cooled engines with automatic electric fans you can often hear the fan start and run for a few moments right after engine shutdown. You don't see the temperature change on the gauge (if any) because the gauge's power is removed when the ignition is shut off.

In the case of a non-fan-forced air cooled engine - most air cooled motorcycles - the last couple of moments of idle as you ease into the parking space or garage generate heat from the running engine, but no airflow for cooling. Same thing happens idling in traffic. That heat contributes to heat soak.

A classic example of heat soak was the R4360 "corncob" radial engine used in the B-36 bomber. It was buried inside the wing of the airplane, and was fan-cooled. It frequently happened than an engine which had been running perfectly at landing would have problems on start-up because of the heat soak.

Another comment here.

I noticed while trying to tune the carb,  If I leaned out the setup, the bike ran hotter.   Which, of coure took longer to cool down.   Got a little better MPG.   But ..... being I bought the bike dirt cheap with a melted piston, I opted for cooler running.  Seem to go better too.  Could be my imagination......

Yeah melted plastic is one thing, but melted finger is really hard to get off the pipe.