MineOS relies on the Linux $PATH variable to decide which Java to use.
In most cases, if upgrading Java, that means the existing Java installation is removed and a new one is put in its place. Then, when invoking Java, whichever is found first is used. Here’s how you can tell which Java is used from the command line:
mc@mineos ~$ which java
/usr/bin/java
If which returns a value, it is being used by MineOS. Check it’s the version you expect, too:
mc@mineos ~$ java -version
openjdk version "1.8.0_102"
OpenJDK Runtime Environment (build 1.8.0_102-8u102-b14.1-1~bpo8+1-b14)
OpenJDK 64-Bit Server VM (build 25.102-b14, mixed mode)
If you still can’t get servers to start, let us know:
a) what distro you’re using
b) how java WAS installed and generally what method did you use to upgrade it (downloaded it manually? apt-get?)
c) as your non-root user, can you start up the Minecraft instance yourself? (the paths are in the webui)