I've modified a few MU installs and as far as I know, this is the first time that the line has caused problems with my layout:
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
When I remove that line, everything is fine as far as I can see. The problem is that when that line is in the header, it moves my divs down a few lines.