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Well, the problem going away on restart is because it probably recalibrates the touchscreen on each boot. Capacitive touchscreens can be really really tricky. Their sensitivity can fluctuate drastically depending on humidity and temperature. Touchscreens only work correctly when they are calibrated in a neutral state, ie nothing touching it. If something is touching it, the neutral point of the touchscreen is thrown completely off. Then, when you remove your finger after the calibration, it causes it to sense a negative capacitance on the screen. Minor fluctuations that under normal circumstances would appear as noise now all of a sudden becomes the dominant signal. This leads to apparently random and unrequested touches.
As to the third-party chargers, they could be improperly grounding the Pre. When the Pre was turned on, it was calibrated with its own ground reference (generally floating, since its battery operated). When connected to the charger, it could pull down the ground to a lower voltage. This would make the touchscreen hypersensitive, so that background noise now becomes the dominant signal.
Edit: Actually, it might be pulling the ground up. I'm not a full-blown electrical engineer specializing in touchscreens, so don't quote me on this.
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