No issues here... Server 2012 R2, FM Server 15v1, Java 8u91. Our server is pretty well patched, Haven't done the October ones yet.
Have you tried removing and reinstalling just Java?
You could probably waste a lot of time trying to fix it, do you have reference to your current setup so you could remove and updated to version 15?
I know you said you cant save the schedules as you don't have console access, are you running custom schedules? ive only ever used the schedules that kamar provides. the other things are pretty basic, just the paths to the database really.
It doesn't take 8 hours to update filemaker server, maybe an hour all up.