It looks like images have actually been substituted for different images, and I can't imagine Flash Builder actually building graphics!
Most likely is some kind of collision between names of classes in different SWC files.
Are you using more than one SWC library in your Flash Builder project?
Are you defining display classes in your Flash Builder project that share similar package name, class name etc?
Have you tried a new FB project that _only_ has this SWC?
I did test with a very simple project using only one swc. In the graphic shown at the top of the page, the fourth object from the right "text swc new" is the result. The first object "from fla" is the output from Flash Pro (and the same from FB 4.6). There are still problems in the render: the filters seem to be problematic.
I have re-installed FB 4.6 and will use it for everything but mobile development as everything renders correctly in 4.6.