You might want to look under which user splunkd is running and how this users privileges match for the directories / files of those apps that do not behave well.
In Linux you could start with:
ps -Af | grep splunkd | grep -v grep
and then look who can do what with the all apps main directories:
ls -la $SPLUNK_HOME$/etc/apps
or drill it down to a specific file:
find $SPLUNK_HOME$/etc/apps/*/*/savedsearches.conf -exec ls -la {} \;
Cheerz - B
Edit
Maybe this helps: http://answers.splunk.com/answering/222327/view.html
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