DIY Midi Fighter - Software conflicts

Hello everybody!
First post here, after a DIY built of my Midi Fighter now I got to the sofware/programming part and I'm having some conflicts and doubts so I hope you can help and that this thread will help somebody else having the same trouble.
So this is the built:
IMG_20130708_113707.jpg
I started this build based on this instructable (http://www.instructables.com/id/Arca...troller/#step1), but I added some more arcade buttons and I used a Funduino Mega 2560 and everything went pretty good until it got to the software part.
I connected the board with the USB cable, I installed the drivers for the device then I used Yoke as described then MIDI-Serial Converted, and YES, the green boxes flash green when I move or hit a button, but after a couple of seconds (and I believe after fast pot movement), the RX and TX boxes start flashing red than the software crashes with the message "java platform se binary has stopped working".
In Live I managed to map the send/return pot or even a drum rack, but the response is not linear, the faders seem to have half the run (they actually don't work for half the run, and the other half goes from 100 to 0 as if that was the total lenght of the fader), and then it crashes anyway after a while showing a MIDI conflict box.
Another thing I noticed about the faders is that the screws coming out from them get hot when connected. Not all the time, but sometime I touch them and they are really hot.
Since the built I based mine on was a 3x3 arcade buttons matrix, I had to use some more pins on my board to make it 4x4 but I just took the ground from a button and connected the remaining buttons to other digital I/O pins the board has on another side.


Notes:
Serial port:COM7 (9600bps)
OS:Windows 7

Please let me know if this is a common problem or you have any idea about how to fix this.

Thank you in advance