I am trying out Autopano Giga 3 under Linux (Mint 12 to be exact, which is based on Ubuntu). In general, it installs and runs well and looks really good. Well done!
One of the issues I do have, is that none of the settings, including the registration key, are saved between sessions. So, every time I open APG 3 A2, I have to re-enter the registration key as well as change any settings I want to change from the defaults. The settings are retained during the session, but as soon as I close APG and re-open it, I have to re-enter everything.
I am a bit surprised by this issue as it worked without a problem in APG2.