[SOLVED] Unable to use an emulated controller on Dolphin (LINUX)

[Reboot]

TL;DR: Emulated controllers stop working after launching a game. (applies to all Dolphin versions installed on Linux, except for dolphin 4.0.2+dfsg-2build1)

Solution: remove your current Dolphin version and install dolphin 4.0.2+dfsg-2build1

Here is how:

sudo apt-get remove dolphin-emu
sudo apt-add-repository ppa:dolphin-emu/ppa
sudo apt-get update
sudo apt-get install dolphin-emu=4.0.2+dfsg-2build1


Original message:
First of all, I apologize for if I post this in the wrong section, I have a problem regarding using controllers on Dolphin in Linux.
After I configure my emulated Gamecube controller for Dolphin, it was able to detect any input from the configuration screen. However, after launching any game, Dolphin lost the input of my controller (whilst other programs such as jstest-gtk do show input).
Now after looking  around on the internet, I realized I had to virtually plug the controller in @ Options > Perferences > Gamecube tab. However, the only things listed there were Slot A, Slot B and SP1.
I've been searching for ages on the internet to find a solution for this, but unfortunately I couldn't find an answer.

Can anyone help me?
Screenshot: https://my.mixtape.moe/zhpufl.png

I'm running a laptop with Ubuntu 15.10 64-bit
Dolphin 4.0-Git
3.6GB of available RAM
Intel Core i3-3217U @ 1.80GHz

[JosJuice]

The place where you plug in controllers was Config > GameCube in the past, but now it's in the Controller configuration. You probably have it set up correctly already, because I don't think you can configure the inputs without setting the controller to plugged in.

Are you sure the games you are trying to play support GameCube controllers? GameCube games work fine with them, but only a few Wii games support them.

[Reboot]

The place where you plug in controllers was Config > GameCube in the past, but now it's in the Controller configuration. You probably have it set up correctly already, because I don't think you can configure the inputs without setting the controller to plugged in.

Are you sure the games you are trying to play support GameCube controllers? GameCube games work fine with them, but only a few Wii games support them.

Yes, I am entirely sure I play a Gamecube controller compatible game, as it is a Gamecube game.
Additional information: While the emulation is running on the background, I checked the controller configuration and entirely no input is detected by Dolphin. This stays like this, even after stopping the emulation and restarting Dolphin, until I remap all the buttons / axis.

Even more additional information: I have tried several different controllers now, from a DS3 controller to Xbox 360, they all meet the same fate.
It seems like only keyboard input is what works.

[Reboot]

Anyone who knows how to solve this problem? I've been searching a lot in the meanwhile but I still don't have any luck finding a solution...

[Reboot]

New info: I have freshly installed Ubuntu 15.10 on another laptop I have, without encryption of the hard disk. Now it is able to list the controllers at the Gamecube tab of the Dolphin Configuration screen. I have tested a bunch of controllers, and they all seem to work flawlessy.

TL;DR: (THIS IS FALSE, DISREGARD THIS)
The problem may be occurring due to an encrypted hard disk drive.

[Reboot]

DISREGARD THIS: NOT THE PROBLEM
More: I am not sure if this is true but it might conflict with UEFI. I have installed Linux on both my desktop and primary laptop with UEFI enabled. Of course Dolphin does not work on both of these machines.

[Reboot]

SOLVED: Apparently on the freshly installed secondary laptop I have Dolphin 4.0.2+dfsg-2build1 was installed. I uninstalled Dolphin from all my machines and installed dolphin 4.0.2+dfsg-2build1, and they work perfectly fine in terms of controller support.

Here is how to get dolphin 4.0.2+dfsg-2build1:

sudo apt-get remove dolphin-emu
sudo apt-add-repository ppa:dolphin-emu/ppa
sudo apt-get update
sudo apt-get install dolphin-emu=4.0.2+dfsg-2build1