I'm afraid there is not refresh mechanism. "The self fixing" is a side effect of the fact that the popup is shared, thus the first time content is loaded, it is sized to accommodate it. Then when it is loaded it uses those dimensions for positioning, however, it the next content has totally different size the same as the initial behavior (misalignment) may be observed.
If you don't mind the flashing of the popup you may try re-displaying it - similar to this test page
. However, you may use this on your own risk as it may have unexpected behavior or not work consistently.
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