I am using cs6. It just started happening today, and I even tried past files, like ones from July and May and it's still happening. (and it didn't happen back in July, or May with the files)
I flatten the same way, ctrl/alt/e too. I'm not doing big editing, just soft light layer, some curves, and that's about it. I do flatten the image and do not save until it's flattened too.