It sounds like you have found a bug in Data Modeler.
What version of Data Modeler are you using?
Is there anything reported in the log file? (This is normally file datamodeler.log in folder datamodeler\datamodeler\log.)
If you could tell us more about the design rules you were applying that would probably help to track down the problem.
I am using ORACLE SQL Developer (3.2.20.09) and it has build-in Data Modeler. Oracle SQL Developer Downloads</title><meta name="Title" content="Oracle SQL Developer Downloads…
Java(TM) Platform 1.7.0_25
Oracle IDE 3.2.20.09.87
Versioning Support 3.2.20.09.87
To apply the design rules i did: Tools -> Data Modeler -> Design Rules -> Design Rules -> Design Rules tab -> Expand All -> Apply All
I've used the rules that are already there. I did not create any new ones.
And in the log file are following lines:
2013-10-04 16:43:00,446 [main] INFO DataModelerAddin - Oracle SQL Developer Data Modeler 22.214.171.1240
2013-10-04 17:04:32,697 [main] INFO DataModelerAddin - Oracle SQL Developer Data Modeler 126.96.36.1990
2013-10-04 19:09:49,539 [main] INFO DataModelerAddin - Oracle SQL Developer Data Modeler 188.8.131.520
2013-10-04 23:09:25,579 [main] INFO DataModelerAddin - Oracle SQL Developer Data Modeler 184.108.40.2060
I think the Java version is unlikely to be the cause of the problem.
If you are running on Windows you may be able to get more diagnostics by running SQL Developer from a Windows Command window.
There's more information on how to do this in http://www.thatjeffsmith.com/archive/2012/06/how-to-collect-debug-info-for-oracle-sql-developer/