Your scene config only has entries for scenes 1 and 2, you need another for scene 3.
<CommandClass id="91" name="COMMAND_CLASS_CENTRAL_SCENE" version="1" request_flags="4" innif="true" scenecount="0">
<Instance index="1" />
<Value type="int" genre="system" instance="1" index="0" label="Scene Count" units="" read_only="true" write_only="false" verify_changes="false" poll_intensity="0" min="-2147483648" max="2147483647" value="2" />
<Value type="int" genre="user" instance="1" index="1" label="Bottom Button Scene" units="" read_only="false" write_only="false" verify_changes="false" poll_intensity="0" min="-2147483648" max="2147483647" value="3" />
<Value type="int" genre="user" instance="1" index="2" label="Top Button Scene" units="" read_only="false" write_only="false" verify_changes="false" poll_intensity="0" min="-2147483648" max="2147483647" value="3" />
<Value type="int" genre="user" instance="1" index="3" label="Config Button Scene" units="" read_only="false" write_only="false" verify_changes="false" poll_intensity="0" min="-2147483648" max="2147483647" value="3" />
</CommandClass>
Another user created config files for HA which creates the scene values for you.