There is an ArrayIndexOutOfBounds exception with the latest final build of Flex SDK 4.1 which manifests itself with incremental builds. Hopefully problem is solved!
There is no official full sdk release out there but in order to solve this you should replace mxmlc.jar in libs folder of your existing sdklocation.
Good mxmlc.jar file can be downloaded from: https://bugs.adobe.com/jira/
And the complete Jira issue is at: https://bugs.adobe.com/jira/
Enjoy your incremental builds again :)
(it seams that this occurs when you are using halo and spark components al together only)