Skipped layers

[Reaping miner]

Hello all, yet again a different problem! Occasionally in my prints i observe a "skipped" layer, a layer which seems to be very underextruded. I tried to reprint that model on two more occasions, however to my surprise the skipped layer was in the exact same z-height for all three prints. I just performed a normal maintenance check on the printer. Cleaning rods and lubricating threads, checking if the nuts are still tight etc. I also installed quite some improved plastic parts on the printer. Afterwards i assumed it was over, sighed, and went on with my hobby. 2 Days ago i started to print a new extruder (AndrewBCN's "ultimate wade/gregs accesible extruder") in order to be able to upgrade to a nozzle fan and lighting, and ultimately printing new X axis parts to i can finally fasten my Z-endstop with adjustable endstop "poker"/flag.

Anyway, the next day the print was finished and i noticed a lot of artefacts in the Z-axis, semi repetitive. (See figure1+2)
NOTE: The figures also show a repetitive artefact (Most noticeable one) i have no idea what caused this either, i am open to suggestions!


The skipped layer problem is fairly visible on the second picture.

(I suffered from random layer misalignment etc before i performed my maintenance check so i did not notice when this problem started to occur. The fact that it also only occurs under specific conditions does not help either.)

In combination with my previously failed prints i noticed that these skipped layers occur at the start of each hole through the wall!
The problem occurs as soon as the printer starts printing the infill of the first layer that has a sidewall of the hole. At least, that is one situation in which it happens.
I have been able to confirm this by printing a (2x1.5x2, XYZ) cube with 1 M3 nuttrap + hole and 1 hole. The skip occurs at both first layers in the hole. (I also tried printing another model which also confirmed this, but i am not going to elaborate on that)

It appears that either the print head moves down less than 0.75mm after the Z-hop up of 0.75mm or that the printer does not move up far enough each layer and skips to the correct postion at the Z-hop. (I have noticed overextrusion during 100% infill prints lately, this is alleviated after infilling starts. Yes, the extruder is calibrated. But filament diameter seems to have increased drastically to about 2 mm, but i do not trust my calipers, and 2mm filament would cause loads of other issues i do not experience. Even if this is the case this is unlikely related to the missing gap phenomenon.)

In anticipation of the request for more information, and my pinpointing, the G-code:

G1 Z3.650BLA BLA BLA
BLA BLA BLA


;LAYER:36
G1 F3600 E292.31378
G1 Z4.400                                 //0.75mm Z-hop up
G0 F9000 X80.082 Y48.262 Z3.750          //GOTO position 0.75mm z-hop down w/o extruding
;TYPE:FILL
G1 Z3.750                  //Z-hop already down?
G1 F3600 E294.81378              //Start infill - WRONG Z HEIGHT
G1 F3000 X79.376 Y47.556 E294.82623
G0 F9000 X79.376 Y46.142
G1 F3000 X81.496 Y48.262 E294.86362


Printer thinks it is at z3.750 (Which was in reality too high!)
;LAYER:37
G1 F3600 E299.07808
G1 Z4.500                 //0.75mm Z-hop up
G0 F9000 X79.625 Y48.361 Z3.850         //GOTO position 0.75mm z-hop down w/o extruding
;TYPE:FILL
G1 Z3.850                 // continueing printing as if nothing happened.
G1 F3600 E301.57808             
G1 F3000 X85.769 Y42.216 E301.68646
G0 F9000 X84.355 Y42.216
G1 F3000 X79.376 Y47.195 E301.77428



Over the course of 5-10 layers the printer catches up and fills the z-gap with air/plastic.

Cura Settings (most recent version):

[profile]layer_height = 0.1
wall_thickness = 0.9
retraction_enable = True
solid_layer_thickness = 0.9
fill_density = 30
print_speed = 50
print_temperature = 220
print_temperature2 = 0
print_temperature3 = 0
print_temperature4 = 0
print_temperature5 = 0
print_bed_temperature = 60
support = None
platform_adhesion = None
support_dual_extrusion = Both
wipe_tower = False
wipe_tower_volume = 15
ooze_shield = False
filament_diameter = 1.75
filament_diameter2 = 0
filament_diameter3 = 0
filament_diameter4 = 0
filament_diameter5 = 0
filament_flow = 100.0
nozzle_size = 0.3
retraction_speed = 60.0
retraction_amount = 2.5
retraction_dual_amount = 16.5
retraction_min_travel = 1.5
retraction_combing = All
retraction_minimal_extrusion = 0.02
retraction_hop = 0.75
bottom_thickness = 0.15
layer0_width_factor = 100
object_sink = 0.0
overlap_dual = 0.15
travel_speed = 150.0
bottom_layer_speed = 20
infill_speed = 0
solidarea_speed = 0.0
inset0_speed = 0.0
insetx_speed = 0.0
cool_min_layer_time = 10
fan_enabled = True
skirt_line_count = 2
skirt_gap = 3.0
skirt_minimal_length = 150.0
fan_full_height = 0.5
fan_speed = 100
fan_speed_max = 100
cool_min_feedrate = 10
cool_head_lift = False
solid_top = True
solid_bottom = True
fill_overlap = 15
perimeter_before_infill = False
support_type = Lines
support_angle = 60
support_fill_rate = 15
support_xy_distance = 0.7
support_z_distance = 0.15
spiralize = False
simple_mode = False
brim_line_count = 10
raft_margin = 5.0
raft_line_spacing = 3.0
raft_base_thickness = 0.3
raft_base_linewidth = 1.0
raft_interface_thickness = 0.27
raft_interface_linewidth = 0.4
raft_airgap_all = 0.0
raft_airgap = 0.22
raft_surface_layers = 2
raft_surface_thickness = 0.27
raft_surface_linewidth = 0.4
fix_horrible_union_all_type_a = False
fix_horrible_union_all_type_b = False
fix_horrible_use_open_bits = False
fix_horrible_extensive_stitching = False
plugin_config = 
object_center_x = -1

object_center_y = -1

My setup:
Prusa i3 - Steel, 12V, NEMA17, igus-drylin bearings Rj4JP, Ramps 1.4SB, DRV8825 drivers, M5 threaded rods
Wade-style extruder, E3D V6 PTFE-lined hotend (1.75mm), Mk3 aluminium heatbed. 0.3mm nozzle