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I played around with some examples and I was able to replicate your issue with dbo..object name conversion.
Looks like we try to guess the target name as we do not capture the default database owners. The guess works ok, unless you specify the target name yourself, as in your case.
Using SQL Developer 3.2.2 there is no workaround except the search and replace dbo_databasename in the generation script as you suggested.
Ill work on a better solution for the next release, If SQL Developer is going to guess "dbo" as the user, then it may as well find the specified target name of dbo instead of assuming the default naming conversion.
Thanks for the feedback,
SQL Developer Team.
Thanks for the confirmation. I've never been good at regex or sed, but they might become my new best friend!