In Linux Mint 18 Cinnamon be sure to check /etc/profile.d/jdk_home.sh I renamed this file to jdk_home.sh.old and now my path does not keep getting overridden and I can call java -version and see Java 9 as expected. Even though I correctly selected Java 9 in update-aternatives --config java
this jdk_home.sh file kept overriding the $PATH on boot-up.