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Its not an error message that can go away. You should have a UPS that can last long enough for the software to properly shutdown FMS.
And, have the PowerChute software run the command to shutdown FileMaker.
That is not the problem my UPS will run my computer for over 45 minutes. Filemaker takes aproximately 5 seconds to shut down and I still get an improper shut down message.
How are you shutting it down?
If not already, you should run a batch script that uses command line commands that CLOSE the files first, then STOP the application.