I have the same issue. Pandora's Jar saves only one file. To save another file, I have to restart Pandor's Jar and Firefox. This happens even if I have it set to Cruise Control -- it saves the first file but no more.
I have 7.3.1, the latest versions of Java and Firefox, and Flash 8, on WinXP. I've recently emptied my cache.
Thanks for any advice!