Different acceleration across joints

I have XYZ router. X and Y axes have the same rate of acceleration, 800mm/s/s . Z axis has a bit slower acceleration rate 400mm/s/s.

Now, what suppose to be in [TRAJ] section and MAX_LINEAR_ACCELERATION?
The INI setup for MAX_LINEAR_ACCELERATION is now taken from X and Y axes, 800mm/s/s.

The reason I ask, I can see that during rapid movement of Z axis for safe distance above the part, Z does not seem to finish Z distance, so X or Y movements already started.

What version of LinuxCNC?
That was an issue quite a while back, but normally that should never happen.
TRAJ values are the maximum allowed by any joint/axis, but the separate joint/axis limits should be respected at all times.

Some details:
LinuxCNC Version 2.9.2
Rexroth Servos via EtherCat SoE, 1ms servocycle, command position + position feedback