By 2001 the diesel transmissions should all be the RE series units, meaning the governor circuit (among other circuits) are handled by the computer.
To over simplify - pushing the throttle down raises the throttle pressure in the V/B on one side of a shift valve. As truck speed increases governor pressure increases on the other side of the shift valve and when high enough, performs the shift. Make sure the kickdown cable works freely and that the return spring is in place on the lever on the trans - if the spring is weak or missing or the cable sticks, the throttle pressure stays too high, and the governor pressure can't/doesn't overcome the throttle pressure to shift the truck.
Failing that, in the RE series transmissions the governor pressure is controlled by the speed being read by the speed sensor. There is a transducer to read governor pressure and a solenoid to regulate it. The computer uses this info to apply the desired governor pressure to the shift valves for shifts. A bad speed sensor, transducer or solenoid can cause errant shifts.
So with this info, I would make sure the throttle (kickdown) linkage works correctly. If that doesn't cure the issue, I would have the trans scanned to see if it shows proper speed sensor and transducer inputs.
Hope this helps.