Controller not working in mupen64plus (Input Configuration does not get updated?)

[vbs]

I am using x86 on Ubuntu 16.04. Latest Retropie.

Well I noticed that my XBOX360 controller is not working within mupen64plus. So I decided to go to ES and reconfigure it using the UI. But the problem was not solved.
I noticed that the file /opt/retropie/configs/n64/InputAutoCfg.ini has not been updated after I configured the input in ES. I might be wrong but I assume after configuring the input the script
/opt/retropie/supplementary/emulationstation/scripts/inputconfiguration.sh
should be triggered and refresh all input config files, no?

When I call it manually then I see this and the InputAutoCfg.ini gets rewritten:
vbs@vbs-XS35:~/.emulationstation$ /opt/retropie/supplementary/emulationstation/scripts/inputconfiguration.sh
Input type is 'joystick'.
Configuring 'emulationstation'
Configuring 'mupen64plus'
Configuring 'reicast'
Configuring 'retroarch'

The next piece in the puzzle is that I could swear I once saw a reference to the inputconfiguration.sh inside of es_input.cfg. It was like "<setup>.../bla/inputconfiguration.sh</setup>". So it looked like a command that ES should trigger after configuring inputs.
But currently that entry is missing from my es_input.cfg. It now starts like:

vbs@vbs-XS35:/opt/retropie/configs/all/emulationstation$ cat es_input.cfg
<?xml version="1.0"?>
<inputList>
<inputConfig type="joystick" deviceName="USB,2-axis 8-button gamepad " deviceGUID="03000000830500006020000010010000">
<input name="a" type="button" id="0" value="1"/>
<input name="b" type="button" id="1" value="1"/>
<input name="down" type="axis" id="1" value="1"/>
...

And there is no trace of a reference to inputconfiguration.sh. So suspect that this is the reason that my input config files do not get updated anymore. Any ideas for this?

Thank you!

Addendum:
Well, even after calling inputconfiguration.sh it did NOT work :) Again a bit strange:
In the InputAutoCfg.ini (of mupen) my controller gets mentioned as this:
; Xbox 360 Wireless Receiver (XBOX)_START
[Xbox 360 Wireless Receiver (XBOX)]
plugged = True

But in ES my controller is just called "Xbox 360 Wireless Receiver" (without "XBOX"), so mupen64 complains on startup:
Input Error: No auto-config found for joystick named 'Xbox 360 Wireless Receiver' in InputAutoConfig.ini
(because mupen only knows Xbox 360 Wireless Receiver (XBOX))

Calling inputconfiguration.sh did not fix this. But then I deleted InputAutoConfig.ini and then again ran inputconfiguration.sh and now its ok. InputAutoCfg.ini now contains correctly:
; Xbox 360 Wireless Receiver_START
[Xbox 360 Wireless Receiver]
plugged = True
plugin = 2

I guess thats a bug or something.

[BuZz]

The es_input.cfg must have been removed at some point - there is an configuration option in RetroPie-Setup to reset it (Manage Packages -> Manage Core packages -> Emulation Station -> Configure) or a shortcut via RetroPie-Setup main menu - Configuration/Tools -> Emulationstation

[vbs]

Oh yes, thank you! Sorry, my bad! I actually deleted it yesterday to reset my controllers. I read on the Wiki that deleting es_input.cfg is the way to go. Well, I did not read it to the end it seems:
You need to delete the configurations you've made in /home/pi/.emulationstation/es_input.cfg but IMPORTANT: YOU NEED TO KEEP IN THE FOLLOWING LINES IF YOU WANT AUTOCONFIGURATIONS TO WORK:

[BuZz]

The wiki should probably redirect people to use the menu option. It didn't even have the warning at one point - Sometimes there is out of date info there.