Been wrestling with this same issue for some time, and finally found a workaround.
Using Xcode 7.2.
Not sure exactly why this is happening, but Over Current Context is not an available option. This project was created some time ago, which I have a hunch could be related.

As a test, I created a brand new project, and Over Current Context is an option.

Since deleting and recreating my existing project was out of the question, I ended up doing the following:
Set the Presentation on the segue to Default. This is preparation for the next step.
On the destination view controller scene, set Presentation to Over Current Context within the Attributes Inspector.

I was able to successfully see the parent view controller underneath the semi-transparent modal.
Note:
I'm supporting iOS 8 and above, so I don't have to mess around with setting the modalPresentationStyle on the parent vs. the child.
Failed attempts:
Setting modalPresentationStyle to .OverCurrentContext on the destination view controller in prepareForSegue did not work for me, because the Storyboard setting seemed to override my code.
Setting Defines Context and Provides Context did not seem to make a difference. I'm guessing these could come into play for some app architectures, just not my in my particular project.