No, I've never been able to get the flexmojos:flashbuilder command to work cleanly either. (That's why we essentially just create the metadata ourselves in the Roo addon as part of the 'flex setup' command.)
What I've found to work well is to just do File -> New -> Flex Project and point to the location of your existing project, then tweak the settings as necessary after it's created to get the paths set up to match the conventions of the Flex Mojos.
Jeremy Grelle
Staff Engineer, Web Products Team
SpringSource