Unfortunately, I can only speculate. I suspect that you may be running into problems through the use of multiple QMainWindows. Generally, you'd only want one of those. Might I suggest sticking your OpenGL windows into a QWorkspace, contained within a single QMainWindow? This would allow you to move the windows around inside the application, which may or may not be desirable. It also provides an easy way to add or remove OpenGL views (again, may or may not be desirable in your application).
If you don't want to use a QWorkspace to contain each QGLWidget, just use a QWidget for each QGLWidget (adding whatever else you need to the QWidget). You shouldn't need multiple QMainWindows.
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