Sometimes when I press one of the hot keys for any given train function (ie. A to increase throttle or ; to change brakes) I have to hold the down for a while before the function is actually performed. Other times I press the key and even the slightest tap causes it to bump multiple throttle/brake positions. This is within minutes of each other on the same locomotive. I understand that on locos where you're pushing the throttle up by percentage that you need to hold it down but on notched throttles, one press should equal one notch.
This problem is more distinct when you are trying to play this game without the HUD to increase the immersion. I doubt that the developers will change this so we have to stick with it.
This also depends on how many processes are going on on your computer. Try to miminise by ending unnessary tasks.