JQM 1.2 Popup Positioning Problem on iPad in Home Screen ShortCut Mode

JQM 1.2 Popup Positioning Problem on iPad in Home Screen ShortCut Mode

Popups introduced in jqm1.2 have positioning problems on iPad in Home Screen mode. Opening the same page in normal Safari has popups working fine.
Looks like positioning calculations need to take into account for a different environment in this mode.
Any ideas for workarounds?
Note: You have to add the page concerned to your Home Screen and launch from the shortcut to see the issue