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There is now a forum specifically for Data Modeler topics: SQL Developer Data Modeler
I assume that you are using the latest version (126.96.36.1999).
Provided the model includes some Entities, they should show up in the Logical Model window.
The log file is normally in file datamodeler.log in folder datamodeler\datamodeler\log (unless some other location has been set in the Environment/Log page of the Preferences (accessed from the Tools menu).
The log should at least contain a line like
2012-10-19 11:03:18,457 [main] INFO ApplicationView - Oracle SQL Developer Data Modeler 3.1.3
for each time you start a Data Modeler session.
It is possible that the log is in a read-only location, and so Data Modeler cannot write to it.
In this case I would recommend that you update the Preferences to use a writable location.
Moving question to another forum