Could the new and upcomming version also include the setting of the working directory as currently programs like putty do not read their settings properly as the working directory is not set to . (the directory where the exe resides), but seems to be set to the directory where the menu app is located.
The 1.0.2 Beta release does this. Grab it in the beta forum. (it's also linked from the main Suite page)
Sometimes, the impossible can become possible, if you're awesome!