Can't select games with genesis controller in menu

[Final Theory]

Hi, I just got my Harmony Encore cartridge in the mail and I formatted my SD card and loaded some roms onto it for testing and I came across a problem. My sega genesis controller did not want to work in navigating through the menus and such. Like I couldn't select a game or anything.

 

Please note that I only use a sega genesis controller for playing the atari 2600 games. This is my preference. Actually I'm using a 7800 for all of this. I luckily found an old paddle controller in my closet and when I use this paddle controller I can navigate through the menus and select games just fine, but then I have to switch back to the genesis controller. Doing this every time a pain to play games.

 

Is there a way to overcome this?

Edited October 25, 2017 by Final Theory

[+SpiceWare]

The genesis controller confuses the controller detection routine to thinking a paddle is plugged in. Holding down button B when turning on your Atari will force joystick mode.

[Final Theory]

Wow, thank you so so much. It works perfect now. You are a lifesaver.

[LidLikesIntellivision]

The genesis controller confuses the controller detection routine to thinking a paddle is plugged in. Holding down button B when turning on your Atari will force joystick mode.

Thank you!