Can you reproduce this in one of the included simulation configs?
If yes then please provide a minimal gcode example (ie one that can actually be run when loaded) along with a clear description of when you are stopping the program and tell us what linuxcnc version you are using.
If you cannot reproduce this in a sim config then please also attach your zipped config folder.
As it is I cannot reproduce this on either 2.9 nor on master.
