File:SkippingStepAcceleration.jpg

Thanks to IRC user Sparky who helped identify the solution to this particular issue.

Slic3r acceleration of the Z-Axis caused the first layer of 5 mm cubes to squish together. This was caused by the acceleration being too fast in Marlin. In vanilla Marlin code the offending lines are:

Line 390

1. define DEFAULT_MAX_FEEDRATE {500, 500, 5, 25} // (mm/sec)

Line 391

1. define DEFAULT_MAX_FEEDRATE {500, 500, 5, 25} // (mm/sec)

Line 394

1. define DEFAULT_ACCELERATION 3000 // X, Y, Z and E max acceleration in mm/s^2 for printing moves

Line 395

1. define DEFAULT_RETRACT_ACCELERATION 3000 // X, Y, Z and E max acceleration in mm/s^2 for retracts

Known working values are:

Line 390

1. define DEFAULT_MAX_FEEDRATE {300, 300, 3, 25} // (mm/sec)

Line 391

1. define DEFAULT_MAX_ACCELERATION {1000,1000,5,10000} // X, Y, Z, E maximum start speed for accelerated moves. E default values are good for skeinforge 40+, for older versions raise them a lot.

Line 394

1. define DEFAULT_ACCELERATION 500 // X, Y, Z and E max acceleration in mm/s^2 for printing moves

Line 395

1. define DEFAULT_RETRACT_ACCELERATION 500 // X, Y, Z and E max acceleration in mm/s^2 for retracts