Just a idle curiosity here, but I've wondered if at certain times I'm not seeing all the tweets by the people I follow.
A couple of things have led me to this conclusion:
At the moment I'm on pretty much all day (some days) and I would have thought that with the "N new tweets" messages and the occasional reload I'd see everything, but sometimes I see a tweet which is clearly a reply to something someone else posted earlier when I don't remember seeing it.
There are some people I hardly see any tweets from at all, yet when I check their profiles they have recent activity.
I'll freely admit that I can't remember all the tweets I see during a day, but I'm not following that many active people so I'm fairly likely to remember if X or Y posted.
I should add that I use the web interface (rather than a desktop app or any other feed) to view Twitter and I'm using Google Chrome on Windows-XP (just in case it makes a difference).