Make sure you check for relative paths in all apps!
I also had this problem with sendemail erroring out when I had the following in my server.conf:
[sslConfig]
sslRootCAPath = $SPLUNK_HOME/blah
Changing this to:
sslRootCAPath = /opt/splunk/blah
fixed my issues except on one server where sslRootCAPath was defined in multiple apps. To fix the sendemail problem, I had to change the path in all apps where it was defined with relative paths, even if the apps didn't take precedence or show up in btool.
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