2.1.1 won't open the correct root directory anymore.

I have a directory structure where there is a project inside another project directory. All of the following directories are recognized as "PhpStorm projects."

Dir A
     Dir Aa (development branch)
     Dir Ab (release branch)

In 2.1 I used to be able to open Aa no problem. Now (with 2.1.1), when I open Aa, it opens A as the root in the project pane even though the window caption states that I've opened Aa. It also reads the settings files for Aa but puts them in the context of A. All of the relative paths are wrong for all of my long list of directory excludes since it's going from A, and I need Aa.

Having A marked as a project directory was a mistake to begin with and a solution to my immediate problem is just to fix that. I've removed the .idea directory but there must be something else somewhere.

But, in other IDEs I've had nested projects before and sometimes you really only want to open the sub-project and PhpStorm currently prevents me from only opening the sub-dir. This causes all sorts of issues for opening files by name and doing searches.

Thanks,
Paul