Well, I searched over maven war plugin jira's and foud out that this is actually a bug, introduced in version 2.4 (more at https://issues.apache.org/jira/browse/MWAR-301).
For convenience i quote the work-around pointed out in the jira issue:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.4</version>
<configuration>
...
<filters>
<filter>${project.basedir}/src/main/filters/my-filter.properties</filter>
</filters>
</configuration>
</plugin>
Tried it on my skin and it works.
Anyway i note that if you specify a properties source file in this position (and this is pom-level war plugin declaration, not profile level), this will be read always, i.e. for every build profile you're specifying. Unless you re-declare the war plugin for each build profile and in each profile specify a different set of properties files (a really bad solution, pointed out here only to say that's wrong-way and for the sake of completeness, obviously IMHO), this solution is limited only to the case in which the given properties file must be always read no matter what build profile has been specified.