A second beta is now available. It fixes some minor bugs in the first beta, such as a broken link to the help file, as well as introducing the option to save PopTray.ini to the AppData folder for Vista/Win7 users.
The Ini Storage location is displayed on the defaults page for your FYI in case you want to manually copy your old poptray ini to that folder. Skin files should also be saved to the appdata folder. In some future version I hope to make importing poptray.ini from older versions more automatic.