I read this quickly so I might have missed a detail. I think your describing an issue with recent Flex releases that is described in the fine print somewhere. If you don't have any fonts embedded in the main app and are only bringing in fonts embedded in CSS SWFs, you have to force-link the EmbeddedFontRegistry by adding something like this to the main app's script block.
import mx.core.EmbeddedFontRegistry; EmbeddedFontRegistry;
(Yes, "EmbeddedFontRegistry" is in there twice, once to define the fully qualified name, the other to create a class dependency to force the linking).