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.
That's true of course. But because EaF was the first episode that CBS-D did and at that time it was a trial, they had a lot more time to complete and perfect the look of it. That look was carried over to the subsequent episodes in season 1. From what I've read and understand about the project, HTV was not involved in that development process. They were brought in when CBS-D couldn't complete all the work in time. And since they were working almost independently from CBS-D (with only the Okudas advising both teams) they didn't benefit from CBS's experiences.