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Rather anecdotal on my part but Java has been a real pain when supporting a Filemaker server. Your experience is rather familiar.
"If Java had true garbage collection, most programs would delete themselves upon execution." – Robert Sewell
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FMS is designed to run on a specific Java build. Upgrading is not always a good idea and can cause problems.
Seems like you already picked the best solution...just do Java updates when you're there,
I don't have FMS so I don't understand why Java would ever be a pain.
That's a key point for sure.