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I've not seen that behavior before. You could try upgrading to v4.0.2 and see if you have more luck there.
If you have the same issue, you can run sqldev in 'debug' mode - change the sqldeveloper.conf file, last line, to load the debug vs nondebug conf file and start sqldev. Copy out the log panel.
I have installed v4.0.2 with JDK 1.7.0_55 and, indeed, it seems to work properly.
I like the fact that the process now shows its advance (eg. object 137 of 237) while comparing. Very helpful. Well done.
Thank you for your suggestion and attention.
Fan of www.thatjeffsmith.com, btw.