The same occurs on my IE6.
It is caused by the way the <SELECT> tag (on which Chooser is based) is implemented in IE, which causes it to appear in front of other controls. Our solution is to hide the choosers in IE, while another display which may overlap (such as the Calendar, or a Dialog) is displayed.
While there might be better solutions, they do require a significant development effort.
For best results, use the Firefox browser..