Not sure if you fixed this. But did you check if there is an inputs.conf under $SPLUNK_HOME/etc/system/local? This will override the inputs.conf settings under your custom application.
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By default the scripted inputs are disabled (disabled = 1). Enable the inputs that you want the add-on to monitor by setting the disabled attribute for each input stanza to 0. Be sure to do this editing under local/inputs.conf
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