For example, if your main MXML file is Main.mxml and your code-behind class is MainClass.as, Flex Builder gets confused and thinks that there should be two application configuration files (one for the MXML file and one for the AS file.) If your app.xml file is named Main-app.xml, you'll get an error along the lines of Adobe AIR application is missing the corresponding MainClass-app.xml.
Note that your document class in Flash projects should extend org.gaeswf.flash.BaseApplication and your Application MXML in Flex should be of type org.gaeswf.flex.BaseApplication (if none of this makes any sense to you, see my Flex 3 Code Behind Quick Start.)