On stock trucks, a dual-mass flywheel was used. This consisted of -- you guessed it -- two discs held together by springs. The idea behind it is the spikes caused by the running engine are dampened by the spring in the flywheel, saving wear and tear on your transmission.
The dual-mass setup is a weak link, and as the flywheel begins to wear out, lots of folks switch to a single-mass flywheel. Those same spikes that were dampened by the springs are now getting to the transmission because everything is "directly" connected. The way I think it works is the gear rollover noise you hear is one side of the gears hitting back and forth on the other side of the gear.
I don't know if that's what's really going on, but I always thought that was it....sounds good anyways...