I am going to run out of ideas what might be the problem...
Here are some ways to demonstrate (sorry for not being minimalistic, I have no good idea where could be the problem):
Create a workflow with some data, add the RapidMiner Viewer node. Open the view (after execution), go to the Advanced Charts option and try the De-Pivoted transformation. It will open up a dialog, called Attribute selection. The problem is, it is not responding to the click events till those buttons are first invoked with keys (like moving around with tabs and selecting them with space). Those will work even after recreating the dialog. I was thinking that this might be because of the missing real frame for the views. But I also realized, that this is not a problem for example for the Advanced Charts/Global configuration/Color scheme/Configure... dialog, even though those are really similar (same ancestor, same base class), but it does appear in that dialog's Add new scheme action, and it cannot be used in any way with mouse (but keys still work well).
It seems when the root frame is null (which is the case) a phantom is created (in JDialog's constructor), and I can confirm it is present during debugging.
Do you have an idea what can be the problem? Do others also observe similar problems? (It worth noting that this works like a charm in the native Swing UI of RapidMiner, unfortunately the original sources cannot be used, this is modified slightly.)
PS.: Windows 7 64 bit English, KNIME 2.7.1, nightly RapidMiner integration (but also with RM 5.3 too), bundled JRE, but also tried with JRE 188.8.131.52 with the same results.