I also tried the Cyrax/Nitara thing. When I beat Konquest I went back to the Netherealm, went to the chest I decided not to unlock and they were gone already. I'd like to think they are there for some reason, but I don't think so.
I would concentrate on finding all of the colored keys as well as where/when to use them. Of course, we still have to find a use for things like the Ninja star and Raiden's lightning staff. The ninja star especially. I could halfway understand the Lightning staff not being used for anything else because after you bring it back to Kung Lao he gives you 600 gold, so it could be ajust a left over item like the Shin-Ryu(sp) message left behind in that hut in Earthrealm. The ninja star however, has had absolutely 0 use.
The colored keys are the big mystery now... Where are they all at? What do they unlock? I only have 3 now, and no luck finding the rest.
I wouldn't put too much faith into the Kodex. I can almost guarentee you what it's going to be... You go to the Bradygames site and it has a bunch of pictures. Using the pictures, you decipher a code that says something like "Earthrealm A3". Considering that the rest of the strategy guide is pretty useless, I'm sure it will be something that we have all already found.
Another thing that has me thinking are the trading cards on the special disk. Why have ones for people like Cyrax, Goro, Shao Kahn, etc. if they aren't in the game? Some people say that it means nothing, that they made them just for "telling the history of MK". Ok, possibly, but then where are bio's for people like Shinnok? He was a boss. Why not Motaro? Kintaro? Sheeva, Sektor, etc. etc. Why do those specific characters have bio's while others are left out of the loop? Could be nothing, but it could be something.
Anyway yeah, no one has found a use for those colored keys yet, they have to unlock something.

I'm doing a thorough konquest all over again. I've spent 5 physical days in the village so far.

I tried doing Konquest again for the village, but I accidentaly ran into Bo rai' cho after the last training missin, so it took me beyond the gates of the village. I got mad and stopped for a while.

well i completed konquest again and like jadedragonmeli, they were gone (cyrax&nitara).
however i did find sindels ring h-3 edenia behind a rock, just like some other people have. i dont know why i was able to get the ring this time around. the only difference between the two profiles i made for konquest is..
the first profile: completed all i can possibly come across. unlocked all of krypt, only have 1 of the colored keys (the one found on dead body in netherrealm)
second profile: only unlocked chests in village, have done very few side quests, have gotten four colored keys from the village, and a mystery key from netherrealm.
i was able to get the ring in the second profile.
now its like the game cannot go any further in any of my profiles. i have thoroughly gone throughout every realm and talked to just about every person, and theres nothing left to do. besides the sindels ring for my first profile, and then raidens staff mission.

wIth Sindels ring, you have to pick it up right after you get the mission from Kitana, if you don't do it quickly, it dissapears forever.