I can't speak for atari, but I know that NES has been finicky ever since they updated raspbian for the rpi2. Most people have been able to fix it by specifying a screen resolution in boot config. How is your pi connected to your monitor? (hdmi, vga, composite, etc.)

ok, that's what I figured. I don't know what it is that nes is trying to look at when it's trying to set the resolution, but anytime that there is a converter involved, it messes up.

you need to do:
sudo nano /boot/config.txt

then uncomment (or add) the lines that read:
framebuffer_width=###
framebuffer_height=###

set the width and height accordingly. You may also need set the
hdmi_group=2
hdmi_mode=##

here are the different modes:
hdmi_mode=1 640x350 85 Hz
hdmi_mode=2 640x400 85 Hz
hdmi_mode=3 720x400 85 Hz
hdmi_mode=4 640x480 60 Hz
hdmi_mode=5 640x480 72 Hz
hdmi_mode=6 640x480 75 Hz
hdmi_mode=7 640x480 85 Hz
hdmi_mode=8 800x600 56 Hz
hdmi_mode=9 800x600 60 Hz
hdmi_mode=10 800x600 72 Hz
hdmi_mode=11 800x600 75 Hz
hdmi_mode=12 800x600 85 Hz
hdmi_mode=13 800x600 120 Hz
hdmi_mode=14 848x480 60 Hz
hdmi_mode=15 1024x768 43 Hz DO NOT USE
hdmi_mode=16 1024x768 60 Hz
hdmi_mode=17 1024x768 70 Hz
hdmi_mode=18 1024x768 75 Hz
hdmi_mode=19 1024x768 85 Hz
hdmi_mode=20 1024x768 120 Hz
hdmi_mode=21 1152x864 75 Hz
hdmi_mode=22 1280x768 Reduced blanking
hdmi_mode=23 1280x768 60 Hz
hdmi_mode=24 1280x768 75 Hz
hdmi_mode=25 1280x768 85 Hz
hdmi_mode=26 1280x768 120 Hz Reduced blanking
hdmi_mode=27 1280x800 Reduced blanking
hdmi_mode=28 1280x800 60 Hz
hdmi_mode=29 1280x800 75 Hz
hdmi_mode=30 1280x800 85 Hz
hdmi_mode=31 1280x800 120 Hz Reduced blanking
hdmi_mode=32 1280x960 60 Hz
hdmi_mode=33 1280x960 85 Hz
hdmi_mode=34 1280x960 120 Hz Reduced blanking
hdmi_mode=35 1280x1024 60 Hz
hdmi_mode=36 1280x1024 75 Hz
hdmi_mode=37 1280x1024 85 Hz
hdmi_mode=38 1280x1024 120 Hz Reduced blanking
hdmi_mode=39 1360x768 60 Hz
hdmi_mode=40 1360x768 120 Hz Reduced blanking
hdmi_mode=41 1400x1050 Reduced blanking
hdmi_mode=42 1400x1050 60 Hz
hdmi_mode=43 1400x1050 75 Hz
hdmi_mode=44 1400x1050 85 Hz
hdmi_mode=45 1400x1050 120 Hz Reduced blanking
hdmi_mode=46 1440x900 Reduced blanking
hdmi_mode=47 1440x900 60 Hz
hdmi_mode=48 1440x900 75 Hz
hdmi_mode=49 1440x900 85 Hz
hdmi_mode=50 1440x900 120 Hz Reduced blanking
hdmi_mode=51 1600x1200 60 Hz
hdmi_mode=52 1600x1200 65 Hz
hdmi_mode=53 1600x1200 70 Hz
hdmi_mode=54 1600x1200 75 Hz
hdmi_mode=55 1600x1200 85 Hz
hdmi_mode=56 1600x1200 120 Hz Reduced blanking
hdmi_mode=57 1680x1050 Reduced blanking
hdmi_mode=58 1680x1050 60 Hz
hdmi_mode=59 1680x1050 75 Hz
hdmi_mode=60 1680x1050 85 Hz
hdmi_mode=61 1680x1050 120 Hz Reduced blanking
hdmi_mode=62 1792x1344 60 Hz
hdmi_mode=63 1792x1344 75 Hz
hdmi_mode=64 1792x1344 120 Hz Reduced blanking
hdmi_mode=65 1856x1392 60 Hz
hdmi_mode=66 1856x1392 75 Hz
hdmi_mode=67 1856x1392 120 Hz Reduced blanking
hdmi_mode=68 1920x1200 Reduced blanking
hdmi_mode=69 1920x1200 60 Hz
hdmi_mode=70 1920x1200 75 Hz
hdmi_mode=71 1920x1200 85 Hz
hdmi_mode=72 1920x1200 120 Hz Reduced blanking
hdmi_mode=73 1920x1440 60 Hz
hdmi_mode=74 1920x1440 75 Hz
hdmi_mode=75 1920x1440 120 Hz Reduced blanking
hdmi_mode=76 2560x1600 Reduced blanking
hdmi_mode=77 2560x1600 60 Hz
hdmi_mode=78 2560x1600 75 Hz
hdmi_mode=79 2560x1600 85 Hz
hdmi_mode=80 2560x1600 120 Hz Reduced blanking
hdmi_mode=81 1366x768 60 Hz
hdmi_mode=82 1080p 60 Hz
hdmi_mode=83 1600x900 Reduced blanking
hdmi_mode=84 2048x1152 Reduced blanking
hdmi_mode=85 720p 60 Hz
hdmi_mode=86 1366x768 Reduced blanking

it mostly depends on your monitor. I haven't been able to figure out why some resolutions work and others dont. usually just try the resolutions closest to your screen resolution.