There is a readme file in the sample CI that addresses some of the questions asked in the forums as of late. Here is also a link to the same document that can be found on fhe wiki:
Short answer: Right now Flash doesn't work in a headless environment. It is possible to use a virtual frame bugger to trick flash into running. Right now support for that feature has not been integrated into the CI tasks found in this project, but it will be in a future release. The fluint project (fluint.googlecode.com) did have this feature, so if you needed to make this work int he short term, you could take some pointers from those tasks.