Today i found a solution / workaround inspired by the forum post from kevin_angus. You have to add the following Parameter -Dapple.laf.useScreenMenuBar=true to the JVM for start the second JDeveloper IDE. Normally this happens in the jdev-Darwin.conf file. So i add this parameter in the Project Properties / Run Configuration / Launch Settings / Java Options section.
So it works...but maybe it should be fix in 12c :). Are your interesting in development your own JDeveloper Extension, than take a look at my ADF News Session.