I am still having this problem and I am wondering if I am the only one due to the lack of responses to my post. If you are having the same issue it would mean a lot to me if you would post your experiences and what you might have tried to solve the problem.
One thing I tried and it seems to delay the problem but not solve it is to not leaving the database open on a client computer that is set to go to sleep. This will normaly let me go more like 5 days before I have a problem.
We have no problem with closing files from the server console (Windows 7, 64bit server, java 7 update 25). Try updating Java or repair server installation (run last version installer and select repair).
But we have problem closing Filemaker Client, if user do some work in file and then quickly shutdown filemaker, the crash occurs after all files are closed. No reply from Filemaker support yet?
I doubt, that somebody from Filemaker support will react, because only you will be emailed when i post this.
I updated to Java 7 update 25 today. I update when I see them so do not think I was very far behind. As for FileMaker server repair I just did a fresh install about a month ago and was having the problem before and after. I will report back later if updating Java helped.
One thing I have noticed that seems to be related is that I am unable to disconnect users. I am not able to make sure it works after a reboot right now but will report back.
I have not heard from FileMaker support on this issue yet no.
Unfortunately Filemaker relies on Java for so much and Java is a flaky application and a delicious target for hackers.
All computers must quite Filemaker before yoiu can safely shutdown the server. The reason for this is that these computers have unflushed data in memory that needs to be saved to the server. Also, some little problem might arise by quiting while a connection is still open.
If you want to quit server, there is the option to ask everyone to quit and wait until they do and their computer disappears from the list, or force quit and cause devastating consequences in lost data, etc.
Force quitting Filemaker Pro can also lead to damage, lost data, etc. I used to chase a client's employee around the store with a baseball bat everytime he did during a long update route just so he could send an email.
To be clear I am not having any issues shutting down the server and when I do shutdown the server I always make sure everyone has closed FileMaker.
I realized I did not tell the whole story on disconnecting users. When I go to close down my database so I can copy it to the iPad I first make sure everyone is closed out of the database. I then log into the admin console and try to close the database. Sometimes I notice that even though no user is logged into the database the admin console still shows a user logged in. At this point I try to disconnect them and it never works.
You can try stop server or restart admin console from command line. The output from cmd can be more descriptive. Here is good overview about new processes in Filemaker Server 12:
Some time ago we updated to FileMaker 15 and the problem went away.