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I've build a fiddle of a "bug" that I'm experiencing: http://jsfiddle.net/y4AXb/4/
When a fixed header (bigger than the usual) is used with a data-id, the page is rendered with errors.
I've resolved the issue simply calling $.mobile.activePage.trigger('updatelayout') after page rendering.
I can confirm this issue when using "oversized" headers as persistent toolbars.
But only, if the second page is shown the first time.
May this is caused by the changed markup order when using persistent toolbars.
At those pages, after the first navigation, the header-markup is appendedTo the content-markup
and it seems the header then could not find its closest ui-page to compute and give the page container the needed top-padding.
After reading @MauriceG his comment I figured the cause of the issue is most probably same as #4019
When you inspect the code of the fiddle you'll see that the content comes before the header in the html.
I tested the fiddle from @DGuidi with the changes from PR #4260 and it does fix the issue.
thanks a lot :)
Fixed by commit 0992512.