you shouldn't copy datafiles when the database is open (until unless the database is backed up HOT and the tablespaces are put in backup mode)

Check the Registry and look at the Oracle Service to see if all three databases' registry Services are setup the same way; they should be setup to do both the following --
1. Stop/Start the Service
2. Stop/Start the database instance

Another way to test will be to stop the service and check the alert log to see if it actually shutdown the database; again compare all three databases with this test.