New start

[m_c]

Unless those straight line moves cause an abrupt direction change that creates a corner angle larger than the set corner break angle/corner rounding settings which would force an exact stop, then they shouldn't cause any problems.

Has exact stop mode (G61) been enabled in your controller?
I don't see it in your G-code file, but you could try adding a G64 to the beginning to see if things improve.

[m_c]

And having just run the figures, all is revealed.



The short moves are creating two 180deg turns, which will be triggering exact stops.
And as they're part of a depth change, I'm guessing you need to look at your lead in move settings.