Further to Denny Conn's remark about protein clumping: this is usually called the 'protein break,' and it takes a vigorous rolling boil to make it happen. Apparently the physical action assists the process, as do real (i.e. not pelletized) hops.
Back when I brewed beer from grain, I had to do the boil on an electric range, which limited the amount of heat I could pump into it. I could tell when I got a good protein break by scooping some hot wort into a glass mug (because it has a handle; saves fingers) and having a close squint at it. Between the swirling, floaty bits & pieces, the liquid itself is crystal clear not murky. This is a GOOD THING, though if it doesn't happen the beer mayshould still be drinkable.
Re: whether or not to keep the lid on, that's not a worry. You either leave it off. or deal with a nasty, messy cleanup job. I always adjusted the SG as req'd once it was safely in the primary.