I used to get something like that from the starting gcode "G1 Z5 F5000", where G means move, Z5 is the coordinate, and F5000 means lightspeed. I do not have hyperdrive capable thrusters on my threaded rods, and so, the mundane stepper motor would skip when it attempted F5000. I now have it set to "G1 Z0.35 F100" and I don't have the problem any longer.
This, however, is a superficial solution, and I should really go into the firmware and change the max speed for my axes.
Perhaps try diving into your gcode and change all the F values which are before the X carriage descent and see whether that changes your problem.
In the expert mode of Slic3r you have the option to change the start gcode.