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I vote on this.
If you go to: http://demos.jquerymobile.com/1.4.2/popup/
and press the button 'Position to origin' and then change orientation, then the popup is no longer positioned accordingly to the position but is centered (like Position to window).
@Ruffio this is currently the expected behaviour. The origin may be off-screen upon orientation change, and we don't want to scroll it into view.