The following snippet removes the alt modifier. I found out that removing it resolve the problem of losing the focus in the panda window for example after an alt+tab.
You have to use it after you have opened a window otherwise mouseWatcherNode is None
buttons = base.mouseWatcherNode.getModifierButtons()
buttons.removeButton(buttons.getButton(2))
base.mouseWatcherNode.setModifierButtons(buttons)
base.buttonThrowers[0].node().setModifierButtons(buttons)