Jog "stuck" on, would not respond to E-stop

Not real sure where to put this but I have a rather pressing concern. After running a very long program this weekend ( probably 14k lines and about 50 minutes long), I tried to jog my router in the Z and Y directions. Both of them I just tapped the perspective keys on the keyboard and both of them acted as If I was holding the buttons down and just kept moving. Neither of the axes would respond to direction changes or E-stop on the keyboard or the radio buttons.

What could cause this? Its rather scary to think and this caused my z to crash and press straight through a tool.

I did not run the latency test for very long. And I had a feeling that was the issue with this. I restarted the PC and that seemed to resolve the issue.

I dont get the latency error everytime, but I do get a RTAPI error everynow and then. I did get a "Joint 0 following error" which is my X axis this time while running the program in auto. Ive seen that error come up in manual jogging but never in auto mode. Could this be a latency issue?

I was on the manual page, not MDI.

and this was on 2.3.0 so yes its old and thats probably been fixed. Im in the process of putting a new PC together for it with the latest EMC release. I just want to get some HAL component's working in it, Like adding a Logitech Controller and a probe input.