Most likely the cause is electrical noise going into the LPT-port and triggering the E-stop. Best fix is to find the cause of the noise and make sure it can't get in, in other words proper shielding and grounding. Next best aproach is to add some filtering to the inputs, either by hardware or software.
The software way: Go to Config->General Config, in the upper right hand corner is a box called Debounce Interval, start with a realtively high value, like 1000 and if that works slowly work your way down untill you find the lowest possible value where it still works.
Doing this affects all inputs so if you have homeswitches they may need to be retweaked as the position may shift slightly depending on how much filtering you apply.