Well I didn't use this feature yet, but I have some people successfully using them with FM 6.0.1 (Should be the same with 6.0.0) using the followin notation:
<configuration>
...
<defines>
<property>
<name>CONFIG::debugging</name>
<value>${flex.debug}</value>
</property>
<property>
<name>CONFIG::versionNumber</name>
<value>'${project.version}'</value>
</property>
</defines>
</configuration>
I'd give that a try. So the trick is to use "defines" instead of "defineStatements".
Chris