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I believe this is related to the recent FMS12.0v5 update that had to be installed to address the new security in JAVA update 51.
Given that FMS11 wasn't updated (and is unlikely to be) - then it will not run with the latest JAVA update and your only option is to revert JAVA back to an earlier version or modify some of the JAVA security.
See this thread: https://fmdev.filemaker.com/thread/74132
Thanks Kent. I'm not sure how I missed that thread yesterday, perhaps because I was looking for Server 11, perhaps I was just not being thorough enough. This may have saved me some time, but in our situation the database server had also crashed, users weren't able to access the server from FM Pro. However, I wasn't here at the time things first went wrong so it could be there was more going on than the information I was given. I'm not sure how much time I'll spend trying to sort it out as my next step is to get the server upgraded to 13 and (hopefully) not have to worry about such things again.
Thanks again for the reply.