This issue has been bugging me for a while. I think I have found a solution, but you should try it for yourself to see if it works for you. I have noticed that opening a JPEG, for example, in Photoshop versus Preview is an easy way to see if the problem is affecting your system. It sounds like you have some candidate images that appear blocked up in the deep shadows/blacks - this is what we are trying to cure. In my case, the affected image is rendered correctly in Photoshop but appears blocked in Preview. Same image, with an sRGB or any other color profile embedded, etc.
In the Eizo ColorNavigator software, when you are creating a new profile for your display and manually setting up the various parameters, you get to the last screen (see attached screenshot) where you can name your new profile before you proceed with the calibration and profiling. At that dialog, select the "Customize profile" button. It will take you to a dialog where you can adjust things like the version (as Andrew pointed out above - maybe select v2 if you want here).
What I found was the culprit was the checkbox that is labeled "Reflect Black Level in Tone Curve." UNCHECK THIS BOX and run your calibration and profiling operation again. Ideally, you want to make a profile with the box checked and then repeat the process with the exact same parameters, but without this box checked. Then open an image that shows the blocked shadows and, with the image displayed in Preview, switch between the two profiles (using the System Prefs > Display list). You should see the problem go away with the profile where the black level in tone curve box has been unchecked.
Hope this solves your problem - it has been plaguing me since Mavericks, but it only rears its ugly head every once in a while.
Attached is an example from my machine on an image that displayed the blacks issue and a comparison I made to demonstrate the effect of the above solution.
Kirk