SEASON 5 SPOILER WARNING!!!!
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Ok, I just re-rewatched the opening episode of Season 5 via the "Bonus Material" and it had the writers commenting on what was happening in the episode but they were also commenting on ALL of Season 5, and they said something that I didn't quite realize while watching Season 5 the first time; they said that Daniel kept saying over and over "What happened, happened" and that since we, the viewers, take his word on everything since he's the scientific mind on the show, we believe him. And in the beginning of Season 5 Daniel firmly believes that what happened, happened. Period. But by the end of Season 5 (and this is what I didn't realize until I heard the writers say it just now), is that Daniel is wrong, and slowly realizes it. He realizes that you CAN go back and affect the outcome of a situation.
So....maybe this explains a little of the inconsistencies?? I don't know, I'm just along for the ride.