Ok the universe conspired against me all day yesterday but I'm pretty sure the problem is that Godot by default limits is physics loop to 60 ticks per second so if you're running at a higher framerate than that you can render a frame and run all the frame update code without updating the physics?

I may be wrong about that, but based on everything I've read so far it sounds like that's possible, and it would explain literally every problem I have.