I have the issue that my windows are not really full height in OS X. I'm new to OS X so I don't know if this is new.
Here is an example image:
Watch the few bottom pixels, the background just shows there, because the window ends. This is obviously not the full screen mode for windows like in a separate space but this is the maximize with the option key.
I am on an Early 2013 MacBook Pro Retina if that is relevant. I'm using the smallest scaling so 1650x1050
Edit: Changing the scaling didn't fix the problem.