I too am running into this issue and I can't seem to pinpoint what's actually causing it. I am also a complete noob to Linux. This is actually the very first time I have ever used linux. So please be as simple as you can with you explanations. If need be I am a sucker for studying Glossary's. :D
Pi Model: 3
RetroPie Version Used: 3.8.1
USB Devices connected: 1 keyboard, 1 Xbox 360 wired fightstick controller, 1 Microsoft wireless dongle
Controller used: MadCatz Xbox 360 BrawlPad
Error messages received: N/A
Guide used: Followed 2 guides. One was a
File: N/A
Emulator: N/A
Attachment of config files: Not sure which config. are actually needed?
How to replicate the problem: Basically I have my Retropie in a state the it runs and works flawlessly. Now when trying to add anything to it upon reboot it seems like the whole screen is shifted down except for the UI. Also besides there being the white bar at the top none of my usb devices seems to work and the only way to fix it is by removing the files and rebooting using the terminal from my PC