There are still a couple of bugs in the new trajectory planner, and I believe that you are running smack into one.
github.com/LinuxCNC/linuxcnc/issues/426
Can you try your code again with the new planner disabled and see if it makes a difference?
You can do it by setting this line to zero in your traj section of your ini file
ARC_BLEND_ENABLE = 0
(setting it to 1 turns the new planner back on.)
