I had a problem upgrading Zend Studio from 9.02 to 9.03 on my Mac desktop, so my solution was to drag/drop the old installation into the trash and then download and install 9.03 from scratch. No problems.
So when I decided to upgrade Zend Studio from 9.02 to 9.03 on my Slackware Linux netbook I didn't even bother with the "Check for Updates" route. I simply deleted the ZendStudio directory (rm -rf $HOME/ZendStudio) in $HOME, downloaded the ZendStudio-9.0.3-x86.tar.gz archive, and then unarchived it in $HOME (tar xvfz ZendStudio-9.0.3-x86.tar.gz) and started it up. It refused to run stating one license was already in use before exiting. So I thought, no problem. I'll just get rid of the license and enter it anew. So, I got rid of what I thought was all of the necessary directories and their contents: .zs .ZendStudio
Now when I try to start up Zend Studio the splash screen comes up, it gets to loading com.zend.php.ui and hangs with a large white box in the center of the screen.