Ran into this issue and thought I'd share the solution, as I couldn't find anything on here about a fix. After applying a Java update to my Windows 2012 Server running my JSS, I was unable to restart the underlying Apache Tomcat 8 instance, and could tell from the logs that it was trying to start it's JVM environment in the wrong version of the JRE. There's nothing in the Jamf Pro docs about this scenario, so I did a bit of sleuthing and found this blog post for a completely different product that pointed me in the right direction:
https://communities.bmc.com/docs/DOC-40005
I replaced Tomcat 7 with Tomcat 8 and got where I needed to go:
C:Program FilesJSSTomcatin omcat8w.exe
Update the path under "Java Virtual Machine" and the restart Tomcat in Services Manager.