Raspberry Pi 3
Retropie 4.1
USB Keyboard
USB Zettaguard Wireless Dongle
Bluetooth Controller
5V Fan connected to internal pins for overclock

I am also having this issue. I'm using the Zettaguard wireless dongle and I have two XBOX 360 controllers that connected at first... but now will disconnect randomly either during configuration or immediately after exiting a game (if they last that long--it's been awhile since I've actually been able to configure them). Two controllers is an absolute no-go. Won't work at all.

I have wiped my SD card and reinstalled the Retropie 4.1 software to start over and have uninstalled and reinstalled the xpad driver multiple times as well as trying the Xboxdrv driver. Neither work for me. I have a 2.5A power supply that came with my Canakit off Amazon but I have added a fan to the internal pins of the Pi. I usually have a USB keyboard connected as well and right now I've got a bluetooth controller connected so I can at least play one player games. It's a Matricom G-Pad XYBA from Amazon. I've tried three different XBOX controllers with NEW batteries.

So as the XBOX controller sits and flashes at me endlessly, I will occasionally see the text on screen say that the controller connects and is not configured. This will happen multiple times while I'm using my bluetooth controller to play. So it gets a connection but then loses it...SO FRUSTRATING. When I get connected and try to configure the controller, it will lose connection during the "configure input" mode and my system is frozen. The keyboard won't exit out of this screen and I have to pull the plug. ... Is there a way to hard-connect these controllers by editing a CFG file and forcing the Retropie to keep a connection to the controller?