QGIS » QGIS Application

My guess is that you are calling the message bar directly from inside your thread? If so you can't alter GUI from a non UI thread. You will need to have a signal on your thread to notify the UI and show the message bar there.

Here is an example:

from PyQt4.QtCore import QThread, QObject, pyqtSignal

class Worker(QObject):
    done = pyqtSignal()
    finalResult = pyqtSignal(int)

    def __init__(self, parent=None):
        super(Worker, self).__init__(parent)

    def do_stuff(self):
        l = 0
        for i in range(100):
            l += i
        self.finalResult.emit(l)
        self.done.emit()

    def cleanup(self):
        pass

def result(value):
    iface.messageBar().pushMessage("Done", str(value))

thread = QThread()
worker = Worker()
worker.moveToThread(thread)

worker.done.connect(thread.quit)
worker.finalResult.connect(result)
thread.started.connect(worker.do_stuff)
thread.finished.connect(worker.cleanup)

thread.start()

crash seems not related with thread but:

iface.messageBar().popWidget(self.progressMessageBarItem)
-->>        self.progressMessageBarItem.deleteLater()

I can't deleteLater QgsMessageBarItem because already removed by popWidget (http://qgis.org/api/qgsmessagebar_8cpp_source.html#l00174)