TLDR: problem solved, it was a switch controller
Welcome to the forums @Kettlestick!
What version of Godot are you using? Could you test Godot 3.4 beta 2 to see if the issue still occurs there? Also, has this issue just started occurring recently or has it always been an issue when you use Godot?
I haven't had this issue myself and it sounds rather strange, given rebooting didn't work nor did changing the mouse. At first I thought it would be the mouse driver that is causing the issue, but if changing the mouse didn't fix it then that seems unlikely, unless both mice use the same driver.
Thanks! I really like Godot, and this is the first really strange error I've run into with it. I'm on 3.3.2 (steam installation) and no it hasn't always done this. It started a couple weeks ago. At first I figured it was just something in my code, but then once I really looked into it, I found it wasn't that.
I tried running beta 3 and beta 2 but both had the same issue.
I also tried updating my mouse driver, but that didn't work either.
I tested the same mouse on my surface 4, and that works fine, no flickering. I kind of expected that.
Do you have another input device like a tablet or something running. I find I get conflicts sometimes from that, but it's unusual that it only happens when running Godot.
Fire7side has the answer: I had a switch pro controller plugged in via USB-C. Unplugged that, and that fixed the problem. Should have thought of that, but I just forget all about it. Still an odd thing to happen. Seems like the controller is functioning properly, none of the buttons are held down or anything, but I can easily reproduce it by plugging and unplugging the controller. Well either way, problem solved.
Thanks both of you!