I recently reinstalled Flex Builder 3 on Mac OS X and I ran into an issue I already encountered a few months ago. During the install process, the setup wizard complained about an Eclipse feature that could not be installed correctly. However, the installation finished correctly. Starting Flex Builder proved unfortunately impossible after this installation. Uninstalling Flex Builder properly and completely (hunting down all caches, logs, etc. left on the hard drive) did not help solve the issue.
The solution is very simple: make sure you are using a 32-bits JVM during the installation. I was using Java 6 64-bits by default and this somehow causes the installer to partially fail. After successful installation on a 32-bits JVM, you can safely switch back to your 64-bits JVM and use Flex Builder without any problem.
Stupid InstallAnywhere crap.