@jerrymrivera Please don't bump old forum posts.
Create a new topic and explain your problem, adding the relevant info about your setup, as explained in https://retropie.org.uk/forum/topic/3/read-this-first.

@mikikiki

Is there a way to map a controller as JS0? I've seen a package useful to decide the order of the controllers, but in Retroarch...

There are ways to force an assignment of js0, but unfortunately Daphne actually reads the joystick event order when grabbing control and the event order cannot be changed.

is there a way to use different joystick numbers with Daphne?

Currently there is not. It's an often requested feature, but development on Daphne seems to have slowed down over the years and the project leader has only ever shown a passing interest in the issue to begin with.

Probably using x-arcade as a keyboard (without xarcade2jstick) I could map the keys in daphne

If using Daphne is important to you, this is likely to be your best option. I know it'll be a pain to reassign all the controls, but some control setups don't even have this ability as an option, so you're still coming out ahead in the long run.

http://mheironimus.blogspot.gr/2015/09/linux-support-for-arduino-leonardo.html

Solution Found! For anyone else having problems with Leonardo/Micro problems, it's just a matter of adding a string to the end of the line in /boot/cmdline.txt depending on your setup:

usbhid.quirks=0x2341:0x8036:0x040 (for Leonardo)
usbhid.quirks=0x2341:0x8037:0x040 (for Micro)

Yay!