So the first time I played the game I found 4 fusion cores in the secret room in Kellog's home, now it's become purified water. Also on "The Dig" mission I found a X-01 armor the first time around, just the head and torso, now a T-51.....

I have a feeling it's because of the level I'm at. For example at higher levels what you can buy in the shop suddenly becomes better than at lower levels. The first time around I went into Kellog's room around lv 30 and the dig around 40. This time around I tried doing both early at lv 18 and the drops have totally changed!

Spoilers go in the Spoiler forum, obviously.

Well, yes.

Leveled lists are leveled.

Go figure.

(Sorry, but this is how it's been since morrowind, so it really shouldn't come as a surprise unless you're completely new to the franchise(s). But if you are, then welcome to the joys and pains of the TES/FO games)

Also its not just your lvl that determines loot, since most of it is random so it also comes down to your luck(both ingame stat and RNG luck) and any special perks you might have that impact loot.