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Have any errors been logged to the log file?
This is normally file datamodeler.log in folder datamodeler\datamodeler\log (unless its location has been changed on the Environment/Log page of the Preferences).
There is no information in the log file, the only entry that is in the log file is
2012-10-11 15:33:24,610 [main] INFO ApplicationView - Oracle SQL Developer Data Modeler 126.96.36.1993
This is a very strange problem......
Is there anything obviously different between those Entities that do open and those that do not?
No, those entities are not different from the others and they have worked before.