I've been reading long PDFs in Evince, this has happened daily.

It is separate from the CPU lock I get every once in a while.
In fact, it scrolls pretty energetically, I'd say the CPU was in good form.

Screen protector? Might have been a good idea, bit late now!

I thought of remapping the key function to see if it's the switch or the driver, but Evince doesn't let me.

Sounds like you've got that covered, though, with FBReader activating on keyup. Notice anything different when you do that?