We develop a large application with several modules, assets, and styles. We noticed a discrepancy between our automated build that runs from a script using mxmlc and our dev builds using Flex/Flash Builder. When building using Flex/Flash Builder we had this module that would work fine. When using the build from the command line we would get an error first that "Verify Error #1014 mx:core::MovieClip could not be found" then if we clicked Continue we would get #1065 on several embedded assets. I found several posts saying that static-link-runtime-shared-libraries needed to be set to true. We already had that as a command line argument.
Recently I downloaded SWF Inspector and viewed the contents of the swf from Flex/Flash Builder and mxmlc. I could see that things were missing from the command line build. I hope this post can save at least one person a ton of research. This was our problem. When our main app, App.mxml was compiled to swf we have the argument
We then use -load-externs=$(OutputDirectory)\Flex\report.xml when compiling the rest of our modules. According to the online help for mxmlc, -load-externs using the xml file omits symbols from linking when compiling a swf. We had copied and pasted commands throughout the build script and had -load-externs as an argument when compiling css to swf. This caused classes and assets defined in report.xml to not be in the style swf. Removing -load-externs from the command line arguments for compiling css to swf resolved the issue and the file sizes of our style swf now matches what we get using Flex/Flash Builder.