I would question what you see via *_SOURCE for Oracle supplied code in general. Again, you should not be transferring Oracle supplied code/objects from machine to machine in this manner. If this problem were to happen to user wrapped code, then I agree that Marco should look into it as a bug in PL/SQL Developer, but you've not yet identified such an issue.

All that said, if you are intent on going down the path you are on, you could always write some PL/SQL to read through *_SOURCE for your desired object, build it into a CLOB, output the clob and then transfer it yourself that way. Again, I highly doubt this will work for transferring Oracle supplied code/objects.