As far as the Daily Show goes (and probably the issue with Family Guy), thsi depends on the data that Tivo gets. I used to have a Daily Show season pass too, but I got all those episodes recorded so I changed it to a manual time record. The problem is that Tivo (the company) doesn't know which episodes are new, and I presume that it's because Comedy Central doesn't tell them. That's the only reason I can tell for it happening.

As for Family Guy, I'm not sure what's going on there. I assume the "middle setting" is the one that records both first runs and repeats, in which case it should get all of them. It might be another case like the one I described about the Daily Show. I had that season pass too, though, and didn't have a problem with it. You're getting the one on Cartoon Network, right?

It's funny, Jon Stewart actually joked about this exact thing on one episode. He said something to the effect of "Tivo will give you 8 episodes of this show in one day."