SNES Controller GPIO autofiring on button press

[Vaelor]

Hi there! Hope anyone can help me.
I got an SNES Controller connected to the GPIO-Pins (no USB SNES controller) and installed the gamecon driver.
Running jstest, the controller runs fine - no multiple Button presses. In emulationstation, it seems to do 'autofire'.
Meaning, every Button press results in many Button presses, practically making it impossible to 'press' anything.

I found this Thread: http://blog.petrockblock.com/forums/topic/autofire-on-the-axis/ but it seems pretty old.
On the new Forums (this one), I could not find something similar or a thread with the same Problem.
Since the Thread on the old Forum is.. well, old, I was wondering if there is a fix available I did miss.
The other Thread mentioned the issue also showing up with jstest, which in my case does not happen.

As a test, I set up an old Raspberry Pi B, where the Controller ran fine without 'autofire'.

Is there anything I can do, or do I really have to recompile my kernel for the raspberry with the fix from the Thread?

Pi Model: 3
RetroPie Version: 4.1.5, Manually installed in Raspbian (first try was with the retropie image, same problem)
Built From: Not sure what is meant with that, I had an Empty 32GB SD-Card and copied the image with
dd bs=4M if=2016-11-25-raspbian-jessie.img of=/dev/sdf
USB Devices: Keyboard and Mouse
Controller Used: Original SNES Controller, no USB.
Guide Used: Official RetroPie guide for setting up a GPIO Controller
https://github.com/retropie/retropie-setup/wiki/GPIO-Modules

Update:
I tried to compile my own Kernel with the fix from the thread.
I used this https://www.raspberrypi.org/documentation/linux/kernel/building.md guide.
I compiled locally on the rpi.
Uname -a showed me for the Kernel the todays date. So I guess that part worked. It did not fix my Issue unfortunately.

I trashed the whole installation, reinstalling the current RetroPie-Image, trying to install the old custom Kernel from the Thread, which fails.

Unpacking raspberrypi-bootloader (1.20160322-1) over (1.20161020-1) ...
Replaced by files in installed package raspberrypi-kernel (1.20161020-1) ...
dpkg: dependency problems prevent configuration of raspberrypi-bootloader:
 raspberrypi-kernel (1.20161020-1) breaks raspberrypi-bootloader (<< 1.20160324-1) and is installed.
  Version of raspberrypi-bootloader to be configured is 1.20160322-1.

dpkg: error processing package raspberrypi-bootloader (--install):
 dependency problems - leaving unconfigured
Errors were encountered while processing:
 raspberrypi-bootloader
Error completing: dpkg