IEAK 9 and Editing the Build

When constructing the build like previous, we have a directory path that is built in the beginning.  On all other platforms, when a change is needed to be made to the build, we would point to that location in the IEAK tool and the build settings would appear.  Is there an issues with IEAK9 and the build settings saving, or is editing a build different?

Please advise.  And yes we have to have IE9 cause IE10 is not supported by many of our applications yet :)  Thanks in advance.