http://www.plupload.com/punbb/viewtopic.php?pid=2381#p2381
@E-SPAR, Plupload needs to measure elements to generate file dialog trigger and position it properly, which obviously is not possible on elements having: display:none;. You might want to call refresh, after you show up your dialog.
In case of Plupload UI widget:
$('#uploader').plupload('getUploader').refresh();