A new version of the S4 software package for windows can be found here: ftp://galaxy.sonoma.edu/pub/S4_Windows.zip
Mac and Linux versions should follow as time allows.
The most important feature of this update is that it now supports the newer version of the WiFly chip (RN-131C/RM). If you were using this chip, you must use the new version of the software. This latest package also includes the very latest version of the Arduino environment (1.5.7). Finally, this version has a streamlined process for entering network parameters. New Network Parameters Instructions: Previously, network parameters had to be entered in two places, in the WiFly_Setup sketch and in the All_Sensors sketch. Now, both those sketches draw from a common file called NetworkParameters.cpp. You can get to this file by double-clicking the shortcut in the Arduino folder. Change the various network properties in this file as needed before running either of your sketches.