Hi from this CNC newbie. It will be a while before the UK wakes, so meantime I'll pass on what I think I've read. . .
The recommendation seems to be to run Mach3 or equivalent off a dedicated desktop PC that is as close to a raw vanilla O/S as possible, to avoid the potential for problems, which problems may be similar to what you are suspecting.
Even old laptops that have a parallel port tend to be avoided due to the complications introduced by special laptop software such as power-saving settings. I understand that using a device such as an ESS (Ethernet Smooth Stepper) can dramatically improve the reliability of the PC-Machine interface and think that ESS is favoured by JAZZ. I think Jonathon is a Linux fan.
In short I would try deactivating whatever you can and see what difference it makes.