If you have recently change your monitor setup settings on the computer, say, moving the cintiq to the left side of the main monitor when it used to be on the right side.
Then your pop up settings are appearing on a non existent monitor.
You can fix this by them switching the desktop settings you change back to what they were before, then dragging the windows onto the monitor that didn't change positions, then putting the settings back to the changed ones and dragging them back to your cintiq (I know there was a way to reset all those popups to the current window in MS4 but I have no idea what it is in MS5/CSP)