<flex-config>
	<default-size>
		<width>1000</width>
		<height>600</height>
	</default-size>
	<default-frame-rate>12</default-frame-rate>	
	<default-background-color>0xcccccc</default-background-color>
	<target-player>9.0.28</target-player>
</flex-config>

For those of us still using Flex Builder 3, every time we create a new project, we usually need to right-click the Project and add a parameter called -default-background-color=0xffffff into the compiler settings.  An easier solution is to create an XML file with a name the same as your MXML file.  So for example, if your Flex project is titled barnacles.mxml, then place this config file in the same directory and name it barnacles-config.mxml.

Flex: Adding Compiler Settings using an XML Config File

Flex

XML