You might also look at this.
//this.zIndexvalue=(this.zIndexvalue)? this.zIndexvalue+1 : 100 //z-index value for DHTML window: starts at 0, increments whenever a window has focus
It's been commented out, and even so 100 might not be enough. Perhaps your ads are positioned absolutely their z-index places them above the window. Inspect it all in Firebug to see.