Torque Toolbox multiple builds

I have both T3D 1.0.1 installed and 1.1 Alpha and when I run the 1.1 alpha it seems to pickup on projects that are in my 1.0.1 install directory. Not sure if this is intentional or not, but would be nice to keep it separate for merge/upgrading reasons, as I am sure many people will want to install several versions to compare them.