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This a quite a specific and unique setup you have there ;-) So I can't easily reproduce this, but searching for your error message brought me to the Qt.AA_X11InitThreads flag, that can be set before the QApplication is constructed: http://doc.qt.io/qt-4.8/qt.html
This flag is not being set currently by rqt, so you could try running rqt from source and edit the qt_gui/main.py file at about line 173: https://github.com/ros-visualization/qt_gui_core/blob/groovy-devel/qt_gui/src/qt_gui/main.py#L173
Directly before the line constructing the QApplication instance add a new line setting the mentioned attribute:
QApplication.setAttribute(Qt.AA_X11InitThreads, True)
app = QApplication(argv)
If that solves your problem, you can file a pull request with this change, so it gets tested on other setups and can hopefully be added to the code.
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