I think I got the solution. I added this code to the wp-includes/js/thickbox/thickbox.css
*:first-child+html #TB_window {
position:fixed;
top:10%;
left:50%;}
Only IE7 should be able to read it. I'm not sure about this but for now it seems to work.
The problem causing this seems to be the thickbox.css and this code there:
#TB_window {
position: fixed;
background: #ffffff;
z-index: 102;
color:#000000;
display:none;
border: 4px solid #525252;
text-align:left;
top:50%;
left:50%;
}
For some reason IE doesn't seem to understand the code as the Firefox and other browsers do.