There are several applications in System Settings where legacy properties are not upgraded correctly; their values are not being written from portal-ext.properties to System Settings on upgrade from previous version of Liferay (e.g. 6.1 or 6.2). Some examples:
Application where property values were not upgraded properly
Application where property values were upgraded properly
Tomcat 9.0.6 + MySQL 5.7.19.
Portal master GIT ID: fd743ae1da088a71a7012161e269b8e67a4debb8.