Energon was the series that had a whole episode 'lost', in that it wasn't dubbed to english from the original Japanese version. Episode 33, which had some big fricking plot elements relating to Scorponok and Alpha Q, ended up making the rest of the series harder to follow (worse than it already was).
http://transformers.wikia.com/wiki/R..._Our_Scorponok

So if the box set is said to have 52 episodes, I wonder what is making up for the lost episode, because I can't see Paramount spending the money required to dub it (the word is that it was never dubbed at all), so maybe they are just sub-titling it, or only including 51 episodes (which would be the cheap Paramount thing to do).

Actually, it would be recommended for anyone getting the Energon set, to read through this site for each episode's list of things missing in the english version:
http://transformers.wikia.com/wiki/E..._%28cartoon%29
It helps make more sense of the visual side of things in the series, and is the next best thing to just getting the original Japanese series (Superlink).