from how to brew by john palmer:
"Covering the pot with the lid can help with heat retention and help you achieve your boil, but it can also lead to trouble. Murphy's Law has its own brewing corollary: "If it can boil over, it will boil over." Covering the pot and turning your back on it is the quickest way to achieve a boilover. If you cover the pot, watch it like a hawk.
Once you achieve a boil, only partially cover the pot, if at all. Why? Because in wort there are sulfur compounds that evolve and boil off. If they aren't removed during the boil, the can form dimethyl sulfide which contributes a cooked cabbage or corn-like flavor to the beer. If the cover is left on the pot, or left on such that the condensate from the lid can drip back in, then these flavors will have a much greater chance of showing up in the finished beer."
http://www.howtobrew.com/section1/chapter7-2.html