Apologies for the delay in my response, I figured out a fix shortly after I posted this and only today found the email notification in my spam folder.
Just in case any one else has this issue, I solved the problem by first sending the applet frame to a blank.htm page, then setting the CSS to none and hidden. This solved the problem.
I don't understand your redundancy question, I probably did not explain myself very well. I have a list of results of TIFF images. When a user clicks to view one of the images, it "opens" (visibility:show, display:inline) a div with a frame that contains an applet which displays the image to the user. There are some nav buttons at the top for selecting previous and next images and also a Close button to make the div go away. When the user clicks Close, it then hides the div with CSS visibility:hidden and display:none. This works in every browser I tested except IE9.
In IE9, the applet basically would stay on the screen even after the div that holds it was hidden. You could get around it by clicking anywhere within the background page and then the applet would go away. To fix I simply now load a blank.htm page into the applet frame before setting the CSS visibility and display parameters for hiding.