You know, this does remind me of some problems I was having. In one case a program restarted itself from the beginning, rather than continuing on from Hold; in another case the tool on the Z axis tried to go through the floor. There were others.
But careful investigation showed that by and large, all my problems happened in conjunction with my interacting with the system. Further careful checking showed that they fell into two classes.
Class 1: I forgot to zero the Z-axis after changing tooling.
Class 2: I accidentally bumped the keyboard or the mouse, causing all sorts of havoc with resets, zeroes and edits.
I did try to blame the machine, but long experience with computer systems told me otherwise. It was an operator effect. (That's me.) And in every case of course, the machine coordinates were correct, even if the user coordinates were ... aberrant. So I learnt (am still learning) to avoid playing with the mouse and the keyboard while the machine is running, and to check every action. In fact, sometimes I deliberately put an M1 after an M6, to make me check.
Now, I am not saying that my problems are the cause of your problems, but one has to wonder. After all, the hiccups seem to happen only after operator action, and certainly not every time. At the very least, it may be worth looking for this.
Cheers