Having same problem as another post. In safari, when a user selects the pop-up window option, it pops up in front for a quick second, disappears to the back for a little bit, pops up infront and continues with the displays and uploads. I applied the fix to the upload_form using...no other changes.
<div id="progress2" style="position: absolute; left: -999px;"><iframe src="about:blank" id="progress2f" name="transfer2" border=0 SCROLLING=NO topmargin=0 leftmargin=0 frameborder=0 style="width: 395px; height: 260px;"></iframe></div>
What it did was pop a blank window upfront, made it fit the whole screen, poped another window and did the upload and displayed correctly, closed and I was left with the first larger pop up window blocking the form. If this makes any sense.