As you may have read on my blog last month, Flex Builder 3 (means 3.0.0) did not work with Ganymede without to have to apply a non official patch to it. It's now fixed with Flex Builder 3.0.1 that cames out monday.
For those who already are on Ganymede and previously have applied the patch, you just need to update your current Flex Builder installation using Eclipse>Help>Search for Flex Builder Updates.
For the others, you have to uninstall Europa (Eclipse 3.3), install Ganymede (Eclipse 3.4), download the last Flex version from the official Flex download place and install it.
Note that the standalone Flex Builder 3.0.1 version is not built on Ganymede, but still on Europa.