Correct @khmarbaise. As usual I found this out after posting the question!
And here's the fix. Add a filter=false resource for binary eg.
<resources>
<resource>
<filtering>true</filtering>
<directory>src/main/resources/</directory>
<includes>
<include>**/*.xml</include>
<include>**/*.properties</include>
</includes>
</resource>
<resource>
<filtering>false</filtering>
<directory>src/main/resources/</directory>
<excludes>
<exclude>**/*.xml</exclude>
<exclude>**/*.properties</exclude>
</excludes>
</resource>
</resources>