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Ultimaker 3D Printer User Guide : Skipped layer / Bed drop



Skipped layer/Bed drop 
Several things can be at play here as different issues can show very similar error in the print - a missing layer.
Underextrusion
One common cause can be temporary underextrusion. Extrusion is prohibited for some reason, such as a tangle on the spool, for a few layers and the printer then continues as normal. See the underextrusion section for more information about this.
Lubrication of z-screw
Another cause can be a lack of lubrication on the z-axis threaded rod. Your printer came with a little bag of accessories, in there you will find a small sachet of green grease that is meant for the threaded rod. Spread out some grease on the rod and move the bed up and down to spread it out thoroughly. It's important that you grab the bed towards the back of the machine while doing this so that you don't risk bending the bed. While doing this it's a good idea to also inspect the screw to see that there isn't some sort of debris causing issues (such as a small piece of PLA for example).
Misalignment of bearings
Next up is some sort of excessive friction causing the bed to bind up until the motor is able to break it free causing a sudden, and too large, drop of the bed. Turn the machine off and manually move the bed up and down to see if you can feel if there is a certain spot that seems to have much higher friction than the rest of the movement.
If you feel that the bed is binding somewhere it could be that the rods are not perfectly aligned with the linear bearings. A classic example of this is a drawer that is pushed in slightly askew, it will bind in place. To remedy this you will have to first remove the cover plate that hides the linear bearings. Two screws on the underside of the bed hold it in place. Once you have removed the screws you can simply lift it to free it. Use a piece of tape to hold it at the top of the printer, out of the way.
Now comes the tedious part. In order to re-align the bearing you need to loosen the four screws that hold each bearing in place. Loosen all but one of the 8 screws. As soon as you've done this it will be hard to move the bed as it will very easily bind in place, patience is key here. Wiggle the bed and move it up and down a bit so that the bearing can self align, tighten one of the screws and then wiggle the platform again and then tighten the two remaining screws. Repeat the same process for the other bearing. Try moving the bed fully up and down and see if you got any improvement. You may have to repeat this once or twice as it can be tricky to get things in just the correct location.
Too much oil
One user reported that he had oiled the two thick rods of the z-stage and this caused issues. Once the oil had been cleaned off again, the problem went away. Worth a try.
Overheating due to excessive current
Due to a slight design flaw of a revision of the controller board it's possible that some printers will have a problem where excess current to the stepper drivers cause issues. What happens is that the stepper drivers overheat, the protection circuitry of the chip kicks in and shuts the driver down for a brief moment, during this moment there's a chance that the bed moves down unpredictably.
Thankfully this is usually easily fixed by simply lowering the current for the stepper motors. This is done on the printer via Maintenance -> Advanced -> Motion settings -> Current Z. The default value is 1300mA, try lowering this to 1200mA.
Faulty rods or bearing
Unfortunately it is also possible that something is wrong with either the rods or linear bearings of the z-stage. If you've tried all the other solutions listed above it might be time to contact your re-seller or Ultimaker themselves to get replacements for these.
Spool holder interference with bed
Check to make sure that the parts of the spool holder that sticks into the machine isn't hitting any part of the z-stage such as the "cap" that goes over the linear bearings or the bed itself. It's possible that you could see some scratch marks on the holder itself.
The easiest way to get around this would be to simply take a file and remove a mm or two from the spool holder tabs. Another, more involved, way to possibly solve it is to move the bed forward. This is done by removing the cover over the linear bearings, loosening the screws on the bearings and then pulling the bed forward. The tricky part here is to get the bearings perfectly aligned with the rods again afterwards. It's very easy for them to start binding if they're not. Using a file will take a minute or two at most so it's a much much less involved process.

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