When you go to start it when it doesn't want to start, don't crank it for more than a few seconds. You'll heat up the starter. BUT first you need to listen carefully for a distinct click noise when you move the key from off to first position, BEFORE you reach the spring loaded 'crank' position. If you don't hear the click the stop solenoid is NOT allowing fuel to flow through the IP to the injectors.
I experience what you are stating, to the extent if I go to restart when the engine is up to operating temp, and I turn the key all the way to crank, the engine SOMETIMES doesn't start, but does crank over, seemingly slightly faster than normal. I usually immediately release the key, then go all the way back to off. Then I turn the key from off to accessories, LISTEN for the click of the solenoid; IF I hear the click, then I go to crank and it will start.
Granted if you follow the above and DON'T hear the click it is possible you may have a beginning of the IP failure, or possibly a loose or otherwise faulty electrical connection at the solenoid/IP, circuit.
Caution if your HST tractor does go to full throttle due to a stuck IP rack- you'll have to starve it for fuel or air/both to stop the engine. To do so you'd have to open your hood and shut off the petcock at the fuel filter bowl, of block intake air at the air filter housing. I think the safest way would be to starve fuel at the filter bowl on the right side of the engine.
Hope this helps, others will likely chime in on this issue. See if you can give us more very specific details of what your procedure has been to date, and results of same.