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If it's working fine after a factory reset, I'd just keep using it and see what happens. The 1% light bug is very well known, and will likely (IMO) be fixed in future firmware.
If you've never had an e-ink device before (and please forgive me if I'm teaching my grandmother to suck eggs here), you do need to often wait a little after input. If you are used to using, say, an iPhone, there is an adjustment period to the reaction time of an eink device. One waiting time that can feel particularly long is the wait for the device to realise that it's been ejected from the computer and that it needs to process the new books that have been put onto it, and give you feedback to that effect. In reality, this wait is only about 10-15 seconds, but it can feel much longer than that! Fiddling about with the device when it's in this sort of waiting period isn't helpful. I'm not saying that this is what you were doing - your device may well have just been a bit hinky out of the box and needed a full factory reset, and I think that was the right thing for you to do.
Lastly, you don't need the Desktop app at all, and back when I used it I found it nothing but trouble. I recommend using wifi for updates.
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