Sometimes I see errors like this if Splunk was started/stopped by root, when it normally runs as a different user. Some of the files become owned by root and then odd things don't work. In Linux, there is a simple fix. Assuming that
Splunk is installed in /opt/splunk
Splunk should run as user splunkit
you are signed in as a user with sudo privileges
sudo chown -R splunkit splunk
Of course, the problem could be something entirely different...