Z-index issues are always tricky to resolve. It's hard to know which elements have a z-index and what's affecting what.
So I wrote a little script that's been very helpful to me. Run it, then click on any element. It will find all of that element's parents that have a z-index set and print them to the dev console. Beware: it will also unbind all your JS bindings, which will probably break your site. I found this useful for elements where propogation was prevented, but if that doesn't work for you, just don't use that line.
You can paste the code directly into your dev tools console, or use this bookmarklet: