I think there could be a number of explanations for this. One, CBS had the advantage of figuring out and perfecting the remastering process when they prepared the sampler disc. When they started work on season 1 they had the experience of working on those three episodes behind them, which HTV obviously didn't. The people at HTV had to perfect the process as they were working on the season, hence the mixed results in the earlier half and the improvement near the end.
This argument does not really hold up. EaF was the first episode CBS-D completed and it looks absolutely fabulous! HTV didn't get anywhere near that level of quality.