In a Flash Builder 4.7 pure Actionscript project I'm using graphics built in Flash Pro and adding the swc to the build path. The output in FB 4.7 looks different than in Flash Pro CS6. I just re-installed both FB 4.7 and FP CS6, and overlaid the latest AIR 3.5 sdk. Still no joy.
I've compiled examples and posted them here: http://cldd.athabascau.ca/learning_activities/FB_Bug/
The image below is a composite showing the same graphic rendered in different projects, the first from FP, the others from FB. They should all look the same.
I re-installed FB 4.6 and built the same projects and all the graphics rendered correctly.