There must be a variable on your end that's caused it. I can tell you with absolute certainty that nothing has been changed in the templates between now and then, having just checked the administration logs and seen that the last change was made on April 29th, and that was by me and completely unrelated to the ads.
The way it's always worked is to resize everything, with the ad visible as it's part of the page, until it reaches just under 800x600. At this point the top menu should hit the LucasForums logo and stop it getting any smaller, and the browser window will start to cut off. The only thing that could cause the cut-off to occur sooner is a large image being present in one of the posts or the header.
Regardless of what you think, I'm not a liar.