I do not believe there is anything you can do at this time to fix this. I had a simple project I had just done to send in a bug report to Apple, but it didn't fail in the demo project as it does in my code. I was going to toss that project away when I saw your problem.
So I have verified that even in the very latest unreleased Xcode and iOS beta this still happens. But, since I had the project already, I did enter a bug report on it with the demo project so Apple can see it for themselves.
15586497 "Keyboard flashes from white to dark under one specific test"
If you want to enter your own bug you can say its a dup of the number above, then no need for a demo project.
IMHO, these things do get fixed, but not for a while - maybe iOS 8 if you're lucky, so I think you're just going to have to live with it, or switch to using a white keyboard.