I think that one should use a dedicated PC (I do so) for the motion controller - turned off all visual candy staff, no anti virus, no active power saving and screen saver. In two words - everything which might take processing power or interfere with the time critical pulse generation is turned off. Using Win XP, Mach3 special driver is written for it primarily.
Laptops have built into their hardware means to save power, CPU throttling and so on. On top of that if the CPU (Intel processors) heats to a near critical temperature it has an internal protection by skipping clock cycles to cool themselves down. Had a problem with this and took me a lot of time until I discovered that the CPU cooler has detached from the holder on one side and the CPU was getting hot.