Check all your settings in the software and make sure there's nothing weird or changed in the settings that might cause it to be interpreting a torch on or off command causing the problem. Check any settings for your ATHC if you have one that could cause an issue. Test by turning off that ATHC and trying a short cut if you can.
Also you could be getting interference from your torch cable and unshielded stepper cables. Separate them from each other as well as any other power cables because I've seen shielding (errr, lack of) cause issues.
Last thought is make sure something isn't overheating driver/electronics wise. Hot electronics can cause strange things to happen too.
You didn't say what machine or equipment you have, but different machines, plasma cutters & ATHC's are connected/cabled differently so can't be more specific, but double check all those to ensure they are correct and good connections.
Let us know if you figure it out, others may learn from you findings.