I'm in the final stages of building an Ultimaker 2 Extended clone (from a project on Thingiverse). I've searched the forum and read various threads on fan issues (seems to be a common problem) but my issue is slightly different. I'm using an E3D V6 hotend, and was planning to use the fixed (non-PWM) 5V output (J34) to power the fan.
First I tried it with the regular Ultimaker 2 Marlin firmware and that didn't work. Then I learned about the Amedee builder, but I already had firmware mostly configured the way I want, so I took the changes from that firmware and applied them to mine to enable that connector but it still isn't working.
One odd thing I noticed is that when the fan should be off (hotend temperature below 40c), I measure 4.9v and when it should be on, I measure 3.6v. The fans never come on in either case. I tested the fans with an external power supply and they work fine. I also checked my cable with an ohm and volt meter and it's good.
I haven't yet gotten the viewer for the schematic files, so I don't know, but I assume that since this is switchable on the 2.1.4 board that there must be a transistor involved. When I first had the fans connected, I unfortunately had the polarity reversed. Did I perhaps blow out a transistor? I don't know what to make of the voltage readings.