To resolve, upgrade to 7.13 or higher.
For versions 7.11 and 7.12, in order to ensure that the server reads the correct configuration file, you can specify the log4j2 configuration file location manually in catalina.properties per the instructions below:
1. Open catalina.properties under the directory "<server-installation>\tomcat\conf"
2. Edit the file and add the below line at the last
log4j.configurationFile=../spotfire-config/log4j2.xml
3. Restart TIBCO Spotfire Server service