I am currently experiencing the same issue, made worse only by the treatment I got at the Apple store in Regent Street in London!!!
I was able to reliably trigger the problem by opening a book in iBooks, placing the window roughly in the top right quadrant of the screen and doing Cmd+F3, which brings up a long, flickering 1-pixel thick line across the screen.
1. I went to the Apple store for the 1st time, we discovered that you could take a screenshot of it, but the 'Genius' wiped the hard drive clean and reinstalled the OS.
2. When I got home I downloaded Chrome and Evernote, without putting ANYTHING else on my machine = the error resurfaced.
3. Took it back to the store, only to find out they had no record of my initial visit, so I had to tell them my life story again, they said they'll replace the logic board, as it appeared to them to be a hardware issue.
4. Heard back from the store, the person told me they had replaced the logic board and the issue had been resolved.
5. Got back to the Apple store and was told that the logic board HADN'T been replaced, and they found it was a software issue, which was resolved. It wasn't - issue was still there.
6. Booked another hopefully actual logic board repair, which was done, got called in and AGAIN THE ISSUE PERSISTED
7. Then the manager of the store said it must be an OS issue, which I don't believe, because ALL THE OTHER MACS in the store don't have that problem.
Back to square one with them but I'm so frustrated with the 'Geniuses' there, who can't seem to grasp the nature of the problem, or couldn't be bothered to read through what is by now page count of repair notes to rival War & Peace. Mega disappointing result - I hope they'll make up for it. I own every apple device under the sun1!!!