Did you see the "use legacy compiler" option? I would recommend finding a way to use the "older" compiler.
One way to do that may be to switch to the Apache Flex SDK. It might cause FB to use the older compiler by default.
Another option is to try the Ant builder options.
I followed the directions here: http://inflagrantedelicto.memoryspiral.com/2012/12/flash-builder-4-7-u seflashsdk/
But the only "Use Specific SDK:" options are Flex 4.6.0 and Flex 3.6a.
When I select Flex 4.6.0 (under "Use Specific SDK:"), I get errors, it seems that some sub classes don't have access to their parents protected methods and properties. The only way to fix this is to delete the project and create it again.
I downloaded the apache flex SDK, and added it via the Flash Builder preferences. Then went into the project and set "Use Specific SDK:" to the appache flex. This brought up more errors, double clicking the errors wouldn't take me to any class, they where mostly something about bitmap...
And the only way to fix it is to delete the project and create it again.
Should I not use Flash 4.6? or not use SWCs? This is really frustrating.
File a bug against Flex at issues.apache.org/jira and attach a simple project that can reproduce the problem, and attach the SWC as well.
I shouldn't post the but with Adobe?
You can try filing a bug with Adobe, but I probably won't see it. My responsibilities are with Apache Flex, not Adobe Flex, and as such, I'm more interested in what problems you had trying to get the SWC working with Apache Flex.