Alert box opens behind app when 'always on top'

I currently have widget-like AIR app which has the option to
stay on top of other windows. It also has slideout 'windows' (DIVs)
with an iframe in it (for the php part). When one is open and 'on
top' has been selected, the alert box (javascript) is displayed
behind that window, so users can't click on ok or cancel to delete
items. I can't make the window smaller either.
Does anyone know how to force the alertbox to display on top
of the widget?
Thank in advance
Stefan

Hi,
Here you go - in the meantime stick a pin in one of the
developers, they should be able to control this behaviour via the
application rather than expecting users to work with freeware - BTW
this is freeware so all the freeware caveats apply (e.g. watch out
you rarely get something for nothing).
http://www.snapfiles.com/get/deskpins.html
'DeskPins allows you to keep any window on top of others with
a few clicks. While many programs offer this as a feature, others
do not, and in such cases DeskPins comes handy. In addition, you
can also define rules that use the window title (with wildcard
support) and can automatically keep any window on top that matches
your rules. The `on top` window is marked with a colored pin that
can be quickly removed by simply clicking on it, returning the
window to its normal state. '

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