3dscapture.com

Thanks for the help everybody!

I went ahead and ordered a pcie USB hub since I had been meaning to for a while now anyways.
I'll mess around with the configuration of my USB devices and I'll post again if I get it working.

It's comforting knowing it's on my PCs end rather than the 3ds itself. The few minutes I messed around with it on my roommates PC it worked amazing. Super stoked to get it up and running

Good news! I got the software working without any flickering.
Turns out it was indeed a USB issue.
However you won't believe what caused it.
Not the headphone DAC, Mic preamp, or any other actually intensive USB devices.
Nope it was the wireless controller adapter I got for my Xbox Elite controller.

Everything works great now with it unplugged!
Thanks again everybody for the help

Came here after I've experienced the same kind of flickering today, after roughly 7 months of light use.
I read the previous post with the xbox controller. Unplugging my own xbox controller seems to have solved it for me, as well.