Let me start off by stating that I have confirmed not every printer's serial connector is wired wrong but at least some are including mine. I will also point you to my previous post about the fan circuitry and what is wrong and why.
http://www.print3dforum.com/showthre...nfigured-wrong
Basically in short form the 2 fans on the extruder housing on some machines may have been wired to the wrong pins on the serial connector. This in turn makes your "print cooling" fan(long ducted one) stay on constantly with no control over it and makes your "extruder cooling" fan(small ducted one on the bottom) only turn on when you tell the software to start cooling your print with your "print cooling" fan. Now this can actually lead to a big problem because your "extruder cooling" fan should always be running and never stop this fan keeps cold air blasting right against your housing and above your hotend. This is to keep a "cold zone" so the heat from your hot end does not travel up your extruder housing and start to heat your filament higher up where it will very easily become soft/melt and deform and then clog and/or jam your printer.
Now there is an easy quick fix way around this and that is to tell the printer to start the "print cooling" fan on the first layer and never turn it off and this will actually have your other "extruder cooling" fan run like it is suppose to. But the proper way to fix this take less then an hour and is pretty easy. Plus you want to have both fans running properly as well so you can turn off that constantly running "print cooling" fan for the first layer or 2 and get good bed adhesion.
First we need to disconnect both the serial connector and stepper motor connector from the extruder housing
Then to get at your serial connections just unscrew the 2 nuts and bolts that clamp the serial connector housing together and they will pop apart with the wiggling.
You will be left with all your wiring for the extruder open. You will also have to peel back about half an inch of the heat shrink covering to be able to have the wires loose enough to to work with. As you can see in the below photo the connections on serial cable go white, green, black, and red(on the front row) and red, yellow, purple, and black(on the back row) We are only going to be working on the front row of connections as they are for the 2 fans in question and in the picture above are wired backwards. The pins on the serial cable are numbered left to right and front to back 1-9 so the front row we will be working on are pins 1-5(but pin 3 has no connection as seen in the photo) and we will be ignoring pins 6-9 on in the back. Pins 1 & 2 are ment for the "extruder cooling" fan and pins 4 & 5 are ment for the "print cooling" fan.
So its really simple and need to be swapped opposite of each other so pin 1 wire will get moved to pin 5 and pin 5 wire moved to pin 1 and the same goes for the 2 other wires to each fan(negative wires). Wire 2 will get moved to pin 4 and wire 4 moved to pin 2. This you can do whatever way you like to solder but I found it easiest to unsolder all 4 pins at once by cutting off the heat shrink first and then lightly touching my soldering tip to each one to pull the wire off the pin and then re-solder each pin one by one in the proper order.
***CAUTION*** REMEMBER YOU MUST PUT NEW HEAT SHRINK OVER EACH CONNECTION TO AVOID ANY POTENTIAL SHORT LATER ON
If done properly your serial connector should run in opposite order now on the front row of connections as red, black, green, and white(like the picture below) I also confirmed this is how it is suppose to be as other members have told me theirs are wired properly this way and others as well have confirmed the same problem I had.
Also side note the wires going to the extruder's motor and wrapped really tight inside the main cable's heat shrink(almost to tight) I choose before assembling the serial connector again to pull back some more of these wires to give slack by keeping them separate from the serial connector housing there is no reason they should be crammed in there anyway and you just risk one of them breaking keeping them pulled/crammed that tight. One member has already had one of their wires break to the stepper motor because of this problem and was having trouble using the extruder properly.
Now connect the serial cable and extruder motor connector back up to your printer and power it up to connect to your software of choice. As long as you did not break any other wires while working and made sure your new solder connections were solid and heat shrinked all should be fine and when you power up your printer you will notice now that your "extruder cooling" fan is now running constantly and your "print cooling" fan is no longer and you can control it full for speed and and on/off time through your software.
I hope this helps someone somewhere down the road.