Has anyone ever seen this issue before?

lol

I would redownload firmware… However I have no Idea of the problem

Same

That actually happened to us yesterday. We were driving and our VEXnet light on the remote started flashing red, but that was the only light visible, the rest were off. The robot worked completely fine. We simply turned the robot off and on, and the lights went back to normal.

Yes. Re-downloading joystick firmware fixes it.

The weird thing about it is that our robot works fine while it’s happening

Could be caused by a low back up battery