That episode you're talking about of Fringe is a season one episode they decided not to air originally. Probably to tighten up the overall story-arc, since it was another one of the episodes that didn't relate to it. The strange thing I found was that the episodes that did air aren't missing an episode number (at least if the number listed on TV.com are the real production numbers).

It was shown this season as a "special" and wasn't intended to try and fit in. They advertised it as a special event but didn't put enough emphasis on it by calling out something like "special lost episode from season one." I believe they used it both as filler and to test audience on that other time slot. It was on a Tuesday, right? Maybe they're planning on trying to put a Fringe/American Idol combo up against Lost next month.

The items mentioned aren't spoilers, since that episode is clearly a season one episode when both the things you mentioned were obviously true.