Hubby got home and I showed the HDX to him. At first he didn't see it. I was like uh oh maybe I am imagining it. so I restarted the HDX and looked again this time in Night Theme which I could plainly see it flicker then handed it to him.
He watched it about 30 seconds then said "That's not a flicker, It's like someone is playing with the brightness. I think your brightness controller is faulty." Which makes sense the auto brightness on this unit has never work right. I would be in the dark when it would suddenly go bright so I disabled it. I originally though it an app issue but I have 4 sideloaded apps on the HDX: Dropbox, ES File Explorer, GoodReads and Mantano.
Cloud apps: Candy Crush Saga, Netflix and Hulu Plus. That's it.
I removed Screen Dim when I found it was no longer needed. I removed WiFi Bar Switch when I saw it wasn't really needed either.
Why only in Books and no where else I have no clue.
It's getting worse with each restart it seems. So glad I called tonight and not waited.