The panel control causes any content under a fixed position footer element not to be rendered.
To achieve this set data-role=footer on a div and then change it's css bottom value (or use a top value) such that the footer shows higher up in the page.
Panel: Set min-height when panel is open. Prevents vertical scrollbar…
…. Fixes #5456 and fixes #5471.
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The panel widget wraps the non-fixed toolbars and content in a div and applies the theme used for the page to this div. When you open a panel the theme of the panel is applied to the page. This is because on many mobile platforms you would see a blink because the panel background isn't rendered yet.
Fixed toolbars aren't wrapped so this means that if you set a top offset for a fixed header you will see the same background as used for the panel above the fixed header.
However, there were issues with the page height when a panel is open. This has just been fixed.
See latest: http://jquerymobile.com/test/docs/demos/panels/panel-nav-form-fixed.html