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Three possible problems that I know of and have dealt with.

EDIT: Holy god I didn't realize this does markdown.... Removed the accidental headers...

-- 1 Does your extruder motor get hot while you print? If so, your vrefs to your motor are probably off.

If this is the case, what is happening is that there is too much juice flowing to the motor which is causing the motor to overheat. Since the motor is touching the cooling block it is also heating the cooling block. The fan and heat sink are unable to cool it faster than it is heating up. This makes the filament that is in the cold end be warm enough that it starts to change state.

Then, if you do a retraction and it pulls the slightly melted filament out and then tries to feed it back in and it bunches up at the top of the cooling block and clogs. Fixing the vrefs on your mainboard will fix this problem. I'm in too much of a hurry to look for it, but there is a great youtube video that shows how to adjust them.

-- 2 When you are looking at the cold end going into the heating block, can you see the part where it gets narrow before it goes into the heat block or is the cylinder all the way in the heating block so that you can't see the part that gets skinnier.

You should be able to see the top part that gets skinny. If you can't, the top part is screwed too far. That skinny part is to separate the hot end of the extruder with the cold end. If the cold end is butting up against the heating block it is heating the cold end and will cause clogs similar to #1.

If this is the case, take it all apart and put it back together following their instructions. Nozzle first, back it out a quarter turn and then top part in. (I did mine the opposite order once which is how I know about this DERP)

-- 3 The top part of the microswiss and the nozzle aren't screwed together tight enough and some funky shiz is happening in the space between that is causing clogs.

Take it apart and put it back together as in #2.

-- Summary: That describes all of the ways in which I have F'd up and then resolved the issue. Mine is working super awesome now and has for a while. The #1 is probably the largest cause of failure on the Wanhao i3s as their control boards up until at least v2.1 were not dialed in to give the stepper motors the proper amount of juice. My motor was usually somewhere between magma and hell fire before I fixed it.