This is not a problem with linux and has nothing to do with this SDK you installed. It's not a problem at all. If an application is displaying in portrait mode, tap and hold its icon and deselect the checkbox next to "display with magnified screen" and click "OK". Next time you launch the application, it will come out the right way. This question and many others have been answered before in this forum, try to use the search before asking.
Enjoy your Zaurus.
Felipe