When Chrysler transmissions (and, I suspect, many others) are driven from the drive wheels while in neutral, there's still some friction going on inside the transmission itself. Normally, this is not really a concern because the engine would be running, therefore would be driving the transmission fluid (oil) pump, therefore would be providing transmission fluid to cool off those moving parts that are being driven.
The whole reason why it's not advised to go in neutral for more than a few miles, while the engine is turned off, is because there's really nothing that will drive the transmission fluid pump, so those moving parts will tend to overheat and eventually fail.
That noise you're hearing is likely something that expanded due to heat buildup from friction, rubbing against something else that is being driven off the engine, and it goes away because there is now transmission fluid flowing over the overheated parts, cooling them off, and in the process causing them to shrink back to normal size.
Recommended Vehicles : Remco <- You might want to look into something like this, that will pump transmission fluid throughout your transmission, even with the engine turned off. Heck, I might even look into it.