After some conversation on the Adobe forums with an Adobe supporter I finally got the point. There is a routine within the installer which adds the "-clean" parameter to the "eclipse.ini". This switch calls Eclipse to clean itself from installed modules. This is a good thing to cleanup your workspace but this should be handled very sensitive from an advanced user who knows that this parameters should be removed afterwards. But if this is added by an installer script and never removed... for sure my Eclipse always throws errors like "com.adobe... not found" if I tried to do any actions depeding on the Flex Builder. I spent so many hours on that and already quit the fight with it but now I'm very happy that I found this bug of the installer and hope this helps other people who ran into same problem.

The complete conversation on Adobe forums

It's been a week since Adobe Flex Builder 3 beta 3 was released and I just tried to get my copy working. It just took about 20 (very frustrating) times and I'm just most annoyed about it than with any software installation before. I already posted my errors with Eclipse 3.3.1.1 on the official forums but got no response at all. Since the end of the last I had to stop all my work on the PV3Dmodeler because the Flex Build 3 beta 2 was no longer available and so I got no chance.

Today my frustration has reached the limit and I crawled the archive of the Eclipse foundation file repositories and I just found the release of Eclipe 3.2.2. I thought a moment or two, read the system requirements from Adobe and decided to download it. For sure I had to cleanup my system once (after too many times) again from the remaining Eclipse and Flex Builder files. The first time it also failed with a critical message and the notice to view the log file of Eclipse. It contains few errors with terms like "core", etc... Uninstalling, cleaning and unpacking again... Because of "core" error of Eclipse I decided to update the 3.2 release with the main updates and reinstalled Flex Builder... and YEEESSS! It worked!

It'd be nice if someone could have told me this once but I'm so happy now and hope I can get back to work asap. Hopefully this information will help someone to solve this problem!

I'm so excited about the first alpha release of Papervision3D 2.0. I just synced my local files with the SVN repository and crawled through the new structure and elements... and I have to say absolutely amazing job! Thanks to the PV3D team and give us just a few days to do an elementary update on our modeling application. For now I'd like to mention that we'll extend it by the brand new features of: lightning, animation and new materials and objects.