Nice pic, great idea to use the iPad as a signal generator.
So you have precisely one wonky decade, and it behaves identically across channels. Not knowing what's inside the attenuators, I'm not sure whether that's good or bad news.
Hopefully it's a configuration problem rather than identical damage across channels.
In your shoes I'd try turning on the cal menu, and try and find that initialization option. The reasoning is that either you have a config issue due to scuttled NVRAM, or else you need new attenuators. Either way you'll need to re-cal, so you've nothing to lose by trying this.
If you prefer to keep hunting, then I'd do this:
1. Measure the input impedance of both channels at all vertical settings (again). Measure inside the bypass cap for CH2.
2. Measure how the gain control works. When you play with the vertical vernier control, it probably runs through a range of voltages between each 5/2/1 attenuator step.
3. Check the attenuator offset (pin 15/16) - this is the last input to the attenuators I could imagine being messed up by configuration.
Good luck!
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