That picture of the scopes is very helpful. You obviously put some time and thought into this issue.
Any time you see a pair of diagonally opposite motors speed up while the other pair slows down, you are seeing a yaw command. I can see from the picture that you get about a 5 second period where one pair speeds up and the other pair slows down, yet you did not give it a yaw command.
Edit: Oh, was this flying or were you holding it in your hand? If you were holding it in your hand, that is probably the whole yaw issue discussed below. Even a fairly loose USB cable attached to GCS on ground can pull a bit of yaw into it in flight. In a quad, yaw is a very underpowered control, and even holding it with a light touch will cause it to yaw hard. That is what fits the facts the best of all. What does it do when actually flying with no cable attached?
Does it drift much in yaw? What stabilization mode are you using for yaw? We generally recommend "Axis Lock" for yaw to add some stability to yaw. Edit: And axis lock tries even harder than rate to fight your holding hand.
I can see that it consistently needs to run (zero based numbers) motors 0 and 2 at a higher level than 1 and 3. Two possibilities come to mind:
- You are using a different brand/model/size of CW prop vs CCW prop (or different motors or ESC's)
- Loose props. This one sounds a little more likely if it only happens intermittently.
Other notes. For best performance, you should be running ESC's that can handle at least PWM 490Hz updates (and have it configured that way too) and with active braking (light damping) turned on. Without light damping, the motor speed up happens more quickly than the motor slow down, and directional commands (caused by you or stabilization) cause the quad to rise because one pair of motors is commanded to slow down 20% and the other pair to speed up 20%. The speed up happens much faster, and what you have is e.g. -2% and +20% for a net increase in thrust of 9% when the controller thinks it should be getting a 0% net increase. This is very noticeable when you command yaw back and forth. Try it.
So maybe we have at least narrowed down your issue to stabilization causing yaw commands and the lack of light damping in the ESC's making that into an aLtitude gain.