They are one and the same. I remember the box set coming out first. Then Warner released the single discs.
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I think they sound quite good. Better than the original CD transfers by far. The box set is a really nice package and I wish all box sets were made this way. Each individual album is packaged seperately in its original album cover (CD size of course). This is so much better than crammin all the songs on a few discs (like the Police box set). Another great thing: besides all the original Doors albums, you get a an extra disc with some great sounding live cuts. I was lucky to find the whole box set at my local used store for $45.
I must say though, I sure wish they had remastered the whole set as Hybrid SACD's.